Extended-spectrum Beta-lactamase Resistance Genes Research Articles

Antimicrobial Resistance Profile and Extended Spectrum Beta-lactamase Resistance Genes in Escherichia coli from Patients in General Hospital, Karshi, Abuja, Nigeria

Aims: This study investigated the antimicrobial resistance profile and extended spectrum beta-lactamase resistance genes in Escherichia coli of from urine of patients sourced from General Hospital, Karshi, Abuja, Nigeria. Study Design: Cross-sectional study. Place and Duration of Study: Department of Microbiology, Nasarawa State University, Keffi, between August 2022 and February 2023. Methodology: A total of 120 samples were collected from patients. Escherichia coli was isolated from the samples using standard microbiological methods. Antibiotic susceptibility testing was evaluated as described by the Clinical and Laboratory Standards Institute (CLSI). The detection of ESBL production in E. coli isolates was carried out using double disc synergy test. In addition, molecular detection of ESBL genes was carried out using Polymerase Chain Reaction (PCR) method. Results: The prevalence of E. coli was 17.5% (21/120), out of which two (2) of the positive isolates (9.5%) were male, and 19 (90.5%) female. Antibiotic resistances in the isolates in decreasing order were as follows: sulphamethoxazole / trimethoprim (SXT: 81.0%), amoxicillin/clavulanic acid (AMC: 61.9%), ofloxacin (OFX: 66.7%), cefotaxime (CTX: 53.4%), gentamicin (CN: 42.9%), ceftriaxone (CRO: 33.3%), imipenem (IPM: 33.3%), meropenem (MOR: 42.4%), nitrofurantoin (NET: 20.3%) and ciprofloxacin (CIP: 23.8%). The commonest antibiotic resistant resistance phenotype was CIP-OFX-SXT (23.8%). Multiple antibiotic resistance (MAR) was observed in 90.5% (19/21) of the isolates, with the common MAR index being 0.3 (23.8%). Six of the twenty one beta-lactam resistant isolates (28.5%) were confirmed ESBL producers. The 6 ESBL positive isolates carried bla genes as follows: blaTEM (1/6, 16.7%) and blaCTX-M (1/6, 16.7%). blaSHV only was not found in any of the isolates. Conclusion: The E. coli isolates from urine of patients in General Hospital, Karshi, Abuja, Nigeria was less resistant to ciprofloxacin, nitrofurantoin, meropenem and imipenem. This implies that the antibiotics are useful in the treatment of infection caused by E. coli. Also, ESBL-positive E. coli isolates harbored ESBL genes, with blaCTX-M and blaTEM as the most common.

Antimicrobial susceptibility and molecular characteristics of beta-lactam- and fluoroquinolone-resistant E. coli from human clinical samples in Nigeria

This study determined the antimicrobial resistance profiles and molecularly characterized beta-lactam- and fluoroquinolone-resistant E. coli recovered from human clinical samples. Three hundred (300) clinical samples collected from two major tertiary healthcare institutions were analyzed using standard microbiological techniques. Antimicrobial susceptibility testing and phenotypic detection of extended-spectrum beta-lactamase (ESBL) were done by disc diffusion and Double Disk Synergy Test. Molecular characterization for ESBL and fluoroquinolone-resistant genes were done by PCR with specific primers. In total, 44 (14.7%) ESBL-producing E. coli were recovered from human clinical specimens. The recovered isolates were multidrug-resistant with multiple antibiotics resistance index values ranging from 0.5–0.8. Isolates exhibited resistance to sulfamethoxazole/trimethoprim 44 (100%), cefoxitin 42 (95.5%), tetracycline 42 (95.5 %), cefuroxime 41 (93.2%), ciprofloxacin 40 (90.9%), cefotaxime 37 (84.1%), amoxicillin 37 (84.1%), amoxicillin/clavulanic acid 37 (84.1), and ceftazidime 35 (79.5%). BlaTEM 41 (93.2%) ESBL gene was the most predominant gene among the isolates, followed by blaCTX-M 9 (20.5%), and blaSHV 1 (2.3%) genes. Co-existence of blaTEM +blaSHV, blaTEM + blaCTX-M, and blaTEM +blaSHV + blaCTX-M genes was observed in 1 (2.3%), 7 (15.9%), and 4 (9.1%) isolates, respectively. All the fluoroquinolone-resistant isolates harbored aac-lb-6-cr gene while Qnr gene was absent. Association of fluoroquinolone resistance- and β-lactam resistance genes; aac-lb-6-cr + blaTEM + blaSHV + blaCTM was observed in 5 (11.4%) isolates. Our study showed high frequency of ESBL-producing E. coli harboring ESBL and fluoroquinolone resistance genes from human clinical samples in Ebonyi State, Nigeria. The high frequency of multidrug-resistant E. coli in our study is very worrisome and could have significant public health impact such as treatment failures, and possibly death, if not properly managed. It is therefore imperative to establish strong regulative measures and guidelines that would help in curtailing the increasing dissemination of these superbugs in healthcare institutions in Nigeria.

Genetic characterization of ESBL-producing and ciprofloxacin-resistant Escherichia coli from Belgian broilers and pigs.

The increasing number of infections caused by Escherichia coli resistant to clinically important antibiotics is a global concern for human and animal health. High overall levels of extended-spectrum beta-lactamase (ESBL)-producing and ciprofloxacin-resistant (ciproR) Escherichia coli in livestock are reported in Belgium. This cross-sectional study aimed to genotypically characterize and trace ESBL-and ciproR-E. coli of Belgian food-producing animals. A total of 798 fecal samples were collected in a stratified-random sampling design from Belgian broilers and sows. Consequently, 77 ESBL-E. coli and 84 ciproR-E. coli were sequenced using Illumina MiSeq. Minimum inhibitory concentration (MIC) for fluoroquinolones and cephalosporins were determined. Molecular in silico typing, resistance and virulence gene determination, and plasmid identification was performed. Scaffolds harboring ESBL or plasmid-mediated quinolone resistance (PMQR) genes were analyzed to detect mobile genetic elements (MGEs) and plasmid origins. Core genome allelic distances were used to determine genetic relationships among isolates. A variety of E. coli sequence types (ST) (n = 63), resistance genes and virulence profiles was detected. ST10 was the most frequently encountered ST (8.1%, n = 13). The pandemic multidrug-resistant clone ST131 was not detected. Most farms harbored more than one ESBL type, with bla CTX-M-1 (41.6% of ESBL-E. coli) being the most prevalent and bla CTX M-15 (n = 3) being the least prevalent. PMQR genes (15.5%, n = 13) played a limited role in the occurrence of ciproR-E. coli. More importantly, sequential acquisition of mutations in quinolone resistance-determining regions (QRDR) of gyrA and parC led to increasing MICs for fluoroquinolones. GyrA S83L, D87N and ParC S80I mutations were strongly associated with high-level fluoroquinolone resistance. Genetically related isolates identified within the farms or among different farms highlight transmission of resistant E. coli or the presence of a common reservoir. IncI1-I(alpha) replicon type plasmids carried different ESBL genes (bla CTX-M-1, bla CTX-M-32 and bla TEM-52C). In addition, the detection of plasmid replicons with associated insertion sequence (IS) elements and ESBL/PMQR genes in different farms and among several STs (e.g., IncI1-I(alpha)/IncX3) underline that plasmid transmission could be another important contributor to transmission of resistance in these farms. Our findings reveal a multifaceted narrative of transmission pathways. These findings could be relevant in understanding and battling the problem of antibiotic resistance in farms.

Antimicrobial Resistance Profile and Extended Spectrum Beta-Lactamase Resistance Genes in Escherichia coli from Poultry Droppings in Nasarawa, Nigeria

Aims: This study investigated the antimicrobial resistance profile and extended spectrum beta-lactamase resistance genes of Escherichia coli isolated from droppings of from selected poultry farms in Nasarawa, Nigeria.
 Study Design: Investigative
 Place and Duration of Study: Department of Microbiology, Nasarawa State University, Keffi, between November 2019 and February 2020.
 Methodology: A total of 90 samples from poultry droppings were collected from selected farms. Escherichia coli was isolated from the samples using standard cultural and microbiological methods. Antibiotic susceptibility testing and minimum inhibitory concentrations were evaluated as described by the Clinical and Laboratory Standards Institute (CLSI). The detection of extended-spectrum beta-lactamase (ESBL) production in E. coli isolates was carried out using double disc synergy test. In addition, molecular detection of ESBL genes was carried out using Polymerase Chain Reaction (PCR) method.
 Results: The prevalence of E. coli was 100%. Antibiotic resistances of E. coli were recorded as follows: streptomycin (S: 94.4%), sulphamethoxazole / trimethoprim (SXT: 90.0%), ampicillin (AMP: 88.9%), gentamicin (CN: 68.9%), amoxicillin/clavulanic acid (AMC: 55.6%), ciprofloxacin (CIP: 41.1%), cefoxitin (FOX: 35.6%), ceftazidime (CAZ: 34.4%), cefotaxime (CTX: 22.2%), and imipenems (IPM: 17.8%). The most common antibiotic resistant resistance phenotype was AMP-CTX-CAZ-CIP-CN (11.1%). Multiple antibiotic resistance (MAR) was observed in 97.7% (88/90) of the isolates, with the common MAR index being 0.5 (33.3%). Twenty five of the thirty beta-lactam resistant isolates (83.3%) were confirmed ESBL producers. The 25 ESBL positive isolates carried bla genes as follows: blaTEM (11/25, 44.0%) and blaCTX-M (18/25, 72.0%). blaSHV was not found in any isolate.
 Conclusion: E. coli isolated from the droppings of selected poultry farms in Nasarawa were less resistant to imipenem, cefotaxime, ceftazidime and cefoxitin in the study location. This implies that the antibiotics are useful in the treatment of infection caused by E. coli. Also, ESBL-positive E. coli isolates harbored ESBL genes, with blaCTX-M as the most common.

Distribution of ciprofloxacin-resistance genes among ST131 and non-ST131 clones of Escherichia coli isolates with ESBL phenotypes isolated from women with urinary tract infection.

Background and Objectives:Escherichia coli (E. coli) sequence type 131 (ST131) is associated with extended-spectrum beta-lactamase (ESBL) production and fluoroquinolone resistance. This study aimed to investigate the prevalence of ST131, ESBL, and plasmid-mediated quinolone resistance (PMQR) genes in the ciprofloxacin-resistant (CIPR) and ESBL producers from women with UTI.Materials and Methods:The CIP-resistant ESBL producing (CIPR/ESBL+) E. coli isolates were screened for ST131-by specific PCR of mdh and gyrB. The ESBL and PMQR genes were screened by single PCR. The ST131 and non-ST131 isolates were selected to determine the mutations of gyrA and parC using PCR and sequencing, and also their genetic background by the Pasteur-MLST scheme.Results:Overall, 55% (33/60) CIPR/ESBL+ isolates were identified as ST131 (94% O25b-ST131). Resistance rate to ampicillin-sulbactam (70%), aztreonam (97%) and gentamicin (61%), the prevalence of aac(6′)-Ib-cr (66%), bla CTX-M-15 (82%), the profile of qnrS+aac(6′)-Ib-cr (30%), and the double mutation in the parC was significantly higher in ST131 than non- ST131 isolates. The coexistence of PMQR and ESBL genes was found in more than 50% of ST131 and non-ST131 isolates. ST131 isolates differentiated into PST43 and PST506.Conclusion:Management of women with UTI caused by the CIPR/ESBL+ isolates (ST131) co-harbored PMQR, ESBL, and chromosomal mutations, is important for their effective therapy.

Extended Spectrum Beta Lactamase (ESBL), blaTEM,blaSHV and blaCTX-M, Resistance Genes in Community and Healthcare Associated Gram Negative Bacteria from Osun State, Nigeria.

Extended Spectrum Beta Lactamase (ESBL) production in gram negative bacteria confers multiple antibiotic resistance, adversely affecting antimicrobial therapy in infected individuals. ESBLs result from mutations in β-lactamases encoded mainly by the blaTEM,blaSHV and blaCTX-M genes. The prevalence of ESBL producing bacteria has been on the increase globally, especially its upsurge among isolates from community-acquired infections has been observed. To determine ESBL prevalence and identify ESBL genes among clinical isolates in Osun State, Nigeria. A cross-sectional study was carried out from August 2016 - July 2017 in Osun State, Nigeria. Three hundred and sixty Gram-negative bacteria recovered from clinical samples obtained from both community and healthcare-associated infections were tested. They included 147 Escherichia coli (40.8%), 116 Klebsiella spp (32.2%), 44 Pseudomonas aeruginosa (12.2%) and 23 Proteus vulgaris (6.4%) isolates. Others were Acinetobacter baumannii, Serratia rubidae, Citrobacter spp, Enterobacter spp and Salmonella typhi. Disk diffusion antibiotic susceptibility testing was carried out, isolates were screened for ESBL production and confirmed using standard laboratory procedures. ESBLs resistance genes were identified by Polymerase Chain Reaction (PCR). All isolates demonstrated multiple antibiotic resistance. Resistance to ampicillin, amoxicillin with clavulanate and erythromycin was 100%, whereas resistance to Imipenem was very low (5.0%). The overall prevalence of ESBL producers was 41.4% with Klebsiella spp as the highest ESBL producing Enterobacteriacaea. ESBL producers were more prevalent among the hospital pathogens than community pathogens, 58% vs. 29.5% (p=0.003). ESBL genes were detected in all ESBL producers with the blaCTX-M gene predominating (47.0%) followed by blaTEM (30.9%) and blaSHV gene was the least, 22.1%. The blaCTX-M gene was also the most prevalent in the healthcare pathogens (62%) but it accounted for only 25% in those of community origin. A high prevalence of ESBL producing gram-negative organisms occurs both in healthcare and in the community in our environment with the CTX-M variant predominating. Efforts to control the spread of these pathogens should be addressed.

Klinik E.coli İzolatlarında Virulans Faktor Genlerinin ve Geniş Spekturumlu Beta Laktamazların Araştırılması

The aim of this study was to investigate the presence of pap, hly, cnf, sfa, aer and afa virulans genes and extended-spectrum beta lactamase resistance genes in 83 clinical E.coli isolates. In 83 E. coli isolates, sfa, pap, hly, cnf, aer and afa virulence genes and TEM-SHV, CTX-M1 and CTX-M9 wide spectrum beta-lactamase genes were investigated by polymerase chain reaction (PCR) method. Resistance rates of 83 isolates to cefixim, trimethoprim/sulfamethoxazole, piperacillin/tazobactam, amoxicillin/clavulanic acid, ampicillin, ceftriaxone, cefuroxime, cefuroxime axetil, ciprofloxacin, fosfomycin, gentamicin and ceftazidime antibiotics were 65%, 54%, 19%,38, 74%, 75%, 72%, 75%, 68%, 2%, 30%, 49%, respectively. CTX-M1 was the most common extended spectrum beta-lactamase (ESBL) among the ESBL genes investigated in 51 of 83 strains. TEM type beta-lactamase was detected in 33 strains, CTX-M9 and SHV 1 isolates. The most common virulence gene was aer gene and detected in 40 strains, followed by the cnf gene detected in 15 of the isolates. The pap, hly, afa and sfa genes were determined in 15.6%, 12.04%, 9.6% and 15.6% of the isolates, respectively. In addition, 10 different virulence factor gene patterns were observed in 83 E.coli isolates. Virulence gene combinations were observed in 27 strains of aer, 6 strains of cnf-sfa-pap, 1 strains of aer-pap, 2 strains of aer-afa, 6 strains of afa, 3 strain of sfa, 9 strain of aer-cnf-hly, 4 isalates of sfa-pap, 1 strain of hly-pap and 1 strains of pap genes. In conclusion, investigating bacterial pathogenicity associated with UTI will contribute to better medical intervention.

First Sequence Analysis of Genes Mediating Extended-Spectrum Beta-Lactamase (ESBL) bla-TEM, SHV- and CTX-M Production in Isolates of Enterobacteriaceae in Southern Benin

: The production of extended-spectrum beta-lactamase (ESBL) by Enterobacteriaceae is a global public health problem. The present study was carried out on 156 strains of enteric bacteria isolated from urinary and cervicovaginal fluid samples. Identification of the strains was performed using MALDI-TOF MS and antibiotic susceptibility tests by disk diffusion method on Mueller Hinton agar in accordance with the recommendations of the Antibiogram Committee of the French Society for Microbiology. ESBL genes were sought by real time-polymerase chain reaction (RT-PCR) and by gel-based PCR. Gel-based PCR products were used for sequencing of the resistance genes, which were analyzed in the NCBI and Arg Annot databases. Results showed a predominance of Escherichia coli both in the urinary and cervicovaginal fluid samples. Klebsiella pneumoniae was the second most isolated bacterium in the specimens. Sensitivity to antibiotics revealed high levels of cephalosporin resistance but low resistance to carbapenem. No resistance was noted to colistine. The bla-TEM gene was present in Escherichia coli, while bla-SHV was found in Klebsiella pneumoniae and bla-CTX-M was recovered in both strains. Analysis of the sequences revealed that bla-Tem1 was predominant in bla-TEM and bla-CTX-M-15 was most represented by bla-CTX-M. This study confirms the presence of ESBL-producing Enterobacteria in Benin. This was an epidemiological study aimed at detecting cephalosporin resistance in gram-negative Bacillus isolated from urinary tract and genital infections developed by women. Since the advent of molecular biology techniques for the identification of resistance in bacteria including determination of ESBL resistance genes (i.e., TEM, SHV, CTX-M), no study has been conducted to identify the different variants that circulate in Benin by sequencing these resistance genes. This sequencing is essential in order to differentiate the non-ESBL parental enzymes, which is not possible with the commonly used PCR techniques that do not permit differentiation of the point generating different variants of the ESBL genes. The present study then helped to identify those variants, in particular Tem1, SHV1, and CTX-M15, which are most encountered in Benin and around the world.

Real Tennis Elbow

<h3>Abstract</h3> Increased colonisation by antimicrobial resistant organisms is closely associated with international travel. This study investigated the diversity of mobile genetic elements involved with antimicrobial resistance (AMR) gene carriage in extended-spectrum beta-lactamase (ESBL) -producing <i>Escherichia coli</i> that colonised travellers to Laos. Long-read sequencing was used to reconstruct complete plasmid sequences from 49 isolates obtained from the daily stool samples of 23 travellers over a three-week period. This method revealed a collection of 105 distinct plasmids, 38.1% of which carried AMR genes. The plasmids in this population were diverse, mostly unreported and included 38 replicon types, with F-type plasmids (n=22) the most prevalent amongst those carrying AMR genes. Fine-scale analysis of all plasmids identified numerous AMR gene contexts and emphasised the importance of IS elements, specifically members of the IS<i>6</i>/IS<i>26</i> family, in the creation of complex multi-drug resistance regions. We found a concerning convergence of ESBL and colistin resistance determinants, with three plasmids from two different F-type lineages carrying <i>bla</i>_CTX-M and <i>mcr</i> genes. The extensive diversity seen here highlights the worrying probability that stable new vehicles for AMR will evolve in <i>E. coli</i> populations that can disseminate internationally through travel networks. <h3>Impact Statement</h3> The global spread of AMR is closely associated with international travel. AMR is a severe global concern and has compromised treatment options for many bacterial pathogens, among them pathogens carrying ESBL and colistin resistance genes. Colonising MDR organisms have the potential to cause serious consequences. Infections caused by MDR bacteria are associated with longer hospitalisation, poorer patient outcomes, greater mortality, and higher costs compared to infections with susceptible bacteria. This study elucidates the numerous different types of plasmids carrying AMR genes in colonising ESBL-producing <i>E. coli</i> isolates found in faecal samples from in travellers to Vientiane, Laos. Here we add to known databases of AMR plasmids by adding these MDR plasmids found in Southeast Asia, an area of high AMR prevalence. We characterised novel AMR plasmids including complex ESBL (<i>bla</i>_CTX-M) and colistin (<i>mcr</i>) resistance co-carriage plasmids, emphasising the potential exposure of travellers to Laos to a wide variety of mobile genetic elements that may facilitate global AMR spread. This in-depth study has revealed further detail of the numerous factors that may influence AMR transfer, therefore potential routes of AMR spread internationally, and is a step towards finding methods to combat AMR spread. <h3>Data Summary</h3> Long-read sequencing data is available through National Center for Biotechnology Information under the BioProject PRJNA853172. Complete plasmid sequences have been uploaded to GenBank with accession numbers in supplementary S1. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.