ESBL Genes Research Articles

Extended-spectrum beta-lactamase-producing Enterobacterales in human health: Experience from the tricycle project, Ghana.

Vulnerable groups, such as pregnant women, are at increased risk of potentially life-threatening infections with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E) for both mother and newborn. However, data regarding ESBL-E carriage and associated risk factors in Ghanaian pregnant women remain scarce. This study aimed to determine the prevalence of ESBL-E carriage and its associated risk factors among pregnant women attending the antenatal clinic at the Korle Bu Teaching Hospital. A systematic sample of 700 pregnant women with gestational age ≥ 34 weeks attending the antenatal clinic at Korle Bu Teaching Hospital was included in the study. After administering a structured questionnaire to assess potential risk factors associated with ESBL-E carriage, patients were given a sterile stool container to submit at least 1 g of stool specimen. Recovered isolates from faecal specimens were identified using MALDI-TOF-MS technology. These isolates were then subjected to susceptibility testing and ESBL identification. A random subset of 24 ESBL-producing Escherichia coli isolates was whole-genome sequenced on the MiSeq Illumina platform. Risk factors associated with ESBL-E carriage were determined using multivariable logistic regression analysis. Among the 700 pregnant women, 42% (294) carried ESBL-E. The predominant ESBL-producing Enterobacterales were Escherichia coli (95%). Fifty percent (50%) of ESBL-E were multidrug resistant isolates (MDRs). Whole-genome sequencing of 24 ESBL-producing E. coli isolates revealed that blaCTX-M-15 (96%) was the most prevalent ESBL gene type. Notably, most isolates belonged to commensal phylogenetic groups (A, B1, and C; 88%). Having a primary level of education (aOR 1.45, 95% CI 1.05-1.96) and consuming legumes as the main source of protein (aOR 0.17, 0.40-0.83) were significantly associated with intestinal carriage of ESBL-E. This study identified a high prevalence of ESBL-E and MDR-ESBL-E carriage among pregnant women. Our findings underscore the urgent need for public health interventions to control the spread of AMR.

Virulence and Antimicrobial Resistance Patterns of Salmonella spp. Recovered From Migratory and Captive Wild Birds.

Salmonella spp., especially those are resistant to extended-spectrum β-lactamase (ESBL), are considered as major concern to global health due to their emergence and dissemination. The aim of this study was to investigate the virulence and antimicrobial resistance (AMR) profile of Salmonella spp. from migratory and captive wild birds. A total 262 faecal samples were collected, and the identification of Salmonella spp. was carried out using a standard culture and PCR as well as molecular detection of virulence and AMR genes. The overall prevalence of Salmonella was determined to be 30.92% (95% CI = 25.63-36.75). Migratory birds exhibited highest prevalence (38.10%), whereas wild birds in captivity showed a lower prevalence (23.40%). The agfA gene was detected at a higher rate at 24.69%. Salmonella spp. exhibited 100% resistance to tetracycline, followed by 58% ampicillin and 46% streptomycin. In addition, there was a resistance rate to ceftriaxone of 17% and to colistin sulphate of 25%. Interestingly, levofloxacin alone displayed 100% sensitivity across all isolates, while ciprofloxacin and azithromycin showed 73% and 64% sensitivity, respectively. The MAR index was 0.25 and 0.42, and 74.07% of all isolates showed multidrug resistance (MDR). It was shown that migratory and captive wild birds contained ESBL genes blaTEM (94.34% and 49.06%) and blaSHV (13.33% and 10%), respectively. Genes responsible for sulphonamide (sul1) resistance were detected in 13.33% and 79% of wild and migratory birds, respectively. Salmonella has been found in captive wild and migratory birds and could act as reservoirs for the transmission of MDR and ESBL bacteria.

Bacterial Co-Infections and Antibiotic Resistance in Urinary Tract Infection of Covid-19 Patients in Erbil City

The COVID-19 pandemic has raised concerns over secondary infections because it has limited treatment options and empiric antimicrobial treatment poses serious risks of aggravating antimicrobial resistance. Many studies have shown that COVID-19 patients are predisposed to developing secondary infections. The prevalence of urinary tract infections (UTI) was evaluated in 248 patients admitted to different hospitals in Erbil city, Iraq. Results showed 138 (55.65%) patients were positive for bacterial growth, of which 72 isolates of Gram-negative and 66 isolates of Gram-positive bacteria were isolated and identified from the urine of COVID-19 patients depending on the 16S rRNA gene using PCR. The predominant obtained bacteria were Staphylococci species, of which isolates belong to 6 species, and the predominant Gram-negative species was Pseudomonas spp. which belongs to 4 species. Also, their susceptibility to 15 antibiotics was tested and it was found that most of the Gram-negative isolates were highly resistant to ampicillin 66(91.66%), amoxicillin 60(83.33%), cephalexin 52(72.22%) and cefixime 50(69.44%). While the most effective antibiotic was imipenem, and with percentage of 26(36.11%), it also showed variable sensitivity to other antibiotics. For Gram-positive bacteria, the highest resistance was against cefixime 40(60.60%), ampicillin 28(42.42%), and 18(27.27%) for both amoxicillin and ciprofloxacin, while the most effective antibiotic was gentamicin, which showed effectiveness against all the Gram-positive isolates. Another part of the study concerned with detection of the existence of ESBLs genes responsible for antibiotic resistance. The results revealed that all the isolates possessed the 16S rRNA gene, whereas blaTEM and blaCTX-M were found to be the most possessed genes in all the isolates, with a percentage of (88.33%).

Enterobacterales Producing ESBLs and AmpC in Fresh Vegetables from Tebessa City, Algeria.

This study aimed to evaluate the contamination levels of fresh products by ESBLs-producing Enterobacterales (ESBLs-E) or AmpC-producing Enterobacterales and characterize ESBLs genes. A total of 132 samples (67 vegetables and 65 fruits) were collected from markets in Tebessa, eastern Algeria. Among the samples, 16 third-generation cephalosporin-resistant Enterobacterales isolates were identified with a prevalence of 19.40% in vegetable samples, while there was no positive finding in fruit samples. Isolates showed resistance to most β-lactams, and all of them displayed multidrug resistance. Phenotypic tests for ESBLs detection, using double-disk synergy test and double-disk test were positive for 14 strains, including Klebsiella pneumoniae (n = 5), Klebsiella oxytoca (n = 4), Klebsiella terrigena (n = 2), Kluyvera spp. (n = 2), and Enterobacter cloacae (n = 1). Two AmpC-producing strains (Citrobacter freundii and E. cloacae) were identified through the AmpC disk test. Contamination rates of vegetables by ESBLs-E and AmpC-producing Enterobacterales were 19.40% and 2.98%, respectively. PCR results showed the presence of at least one ESBL gene in seven selected strains, with the dominance of blaCTX-M gene. Notably, K. pneumoniae strains showed the co-occurrence of two or three genes. Sequencing identified uncommon variants of ESBLs genes for the first time in Algeria, including blaCTX-M-79 (2/7), blaCTX-M-107 (2/7), blaCTX-M-117 (2/7), blaTEM-112 (1/7), blaTEM-125 (2/7), blaTEM-194 (1/7), and blaSHV-176 (3/7).

Role of heavy metals pollution on emergence of antibiotic co-resistance in E. coli isolates

Background: Heavy metal pollution in water is one of the most serious environmental problems. These findings have prompted the idea that metal-exposed bacteria may have altered resistance to antibiotics. This study was performed to investigate the presence of heavy metal resistance genes (HMRGs) in Escherichia coli.Methods: HMRGs and antibiotic resistance of 100 E. coli from sewage and fresh water were detected by PCR. Minimum inhibitory concentrations (MICs) of heavy metals were determined by the broth micro dilution method. Antibiotic discs used to detect multidrug resistance, was recovered and assembled using third-generation sequencing.Results: The frequency of different HMRGs in E. coli ranged from 1–67%., while prevalence of ESBL genes ranged 5-17% in freshwater isolates, and 54- 96% in swage isolates. MICs of heavy metals for E. coli ranged widely from ≤8.0-800 mg/L. Moreover, HMRGs (PbRT, cadD arsB, PcoA, czrc, and chrA) were found to be significantly associated with one or more ARGs ( tetA, blaTEM, blaSHV and blaCTX) (P < 0.05).Conclusion: In conclusion, HMRGs were widely present in E. coli isolated Dujla river and sewage water were significantly associated with DRGs . It is remarkable that the coexistence of HMRGs, DRGs and ARGs confer co-resistance to heavy metals, and antibiotics.Keywords: Heavy metals; Antibiotic resistance

Genotypic Characterisation and Antimicrobial Resistance of Extended-Spectrum β-Lactamase-Producing Escherichia coli in Humans, Animals, and the Environment from Lusaka, Zambia: Public Health Implications and One Health Surveillance.

Extended-spectrum β-lactamases (ESBL) in Escherichia coli are a serious concern due to their role in developing multidrug resistance (MDR) and difficult-to-treat infections. This study aimed to identify ESBL-carrying E. coli strains from both clinical and environmental sources in Lusaka District, Zambia. This cross-sectional study included 58 ESBL-producing E. coli strains from hospital inpatients, outpatients, and non-hospital environments. Antimicrobial susceptibility was assessed using the Kirby-Bauer disk diffusion method and the VITEK® 2 Compact System, while genotypic analyses utilised the Illumina NextSeq 2000 sequencing platform. Among the strains isolated strains, phylogroup B2 was the most common, with resistant MLST sequence types including ST131, ST167, ST156, and ST69. ESBL genes such as blaTEM-1B, blaCTX-M,blaOXA-1, blaNDM-5, and blaCMY were identified, with ST131 and ST410 being the most common. ST131 exhibited a high prevalence of blaCTX-M-15 and resistance to fluoroquinolones. Clinical and environmental isolates carried blaNDM-5 (3.4%), with clinical isolates showing a higher risk of carbapenemase resistance genes and the frequent occurrence of blaCTX-M and blaTEM variants, especially blaCTX-M-15 in ST131. This study underscores the public health risks of blaCTX-M-15- and blaNDM-5-carrying E. coli. The strengthening antimicrobial stewardship programmes and the continuous surveillance of AMR in clinical and environmental settings are recommended to mitigate the spread of resistant pathogens.

Detection of virulent and ESBL-resistant Salmonella species from cattle and associated farm environment

The aim of this study was to explore the virulence characteristics and antibiotic resistance in Salmonella species isolated from cattle farms. During the study, 10 cattle farms were selected and from each farm, 35 samples consisting of faeces, milk, udder swabs, hand swabs, floor swabs, animal drinking water, pit water, composite fodder sample, and dairy utensil swabs were collected. Accordingly, 350 samples were collected from 10 farms and processed for the detection of Salmonella spp. Presumptive Salmonella isolates were confirmed by PCR and characterized for virulence and antibiotic resistance genes. From 350 samples, 19 (5.40%) Salmonellae were recovered, and out of 19 Salmonellae, 12 were ESBL producers. Similarly, out of 19 isolates, spvC was the predominant gene detected (42.10%), followed by stn (31.5%), and spvR (26.31%), whereas, invA, and iroB genes were detected in all 19 Salmonella isolates. Most of the Salmonella isolates were multi-drug resistant strains exhibiting resistance to nalidixic acid (94.73%), tetracycline (36.84%), and ceftazidime (42.10%). Out of 12 ESBL-positive Salmonellae, 9 (75%) isolates harboured ESBL genes, viz. blaSHV and blaTEM (25% each) and blaCTX-M and blaOXA (16.66% each). Six Salmonella isolates showed the presence of tetA gene. The current study indicated healthy cattle and the associated farm environments could be a source of virulent and drug-resistant Salmonellae. The current study also advocates phenotypic and genotypic antibiotic resistance monitoring at farm animal premises and agricultural ecosystems.

A systematic review and meta-analysis on the prevalence of extended-spectrum beta-Lactamase-Producing Klebsiella Pneumonia in Nigeria

Background: Rapid emergence and proliferation of extended spectrum beta-lactamase producing Klebsiella pneumoniae (ESBL-KP) constitute a serious health problem globally. Objectives: The aim of this study was to evaluate the pooled prevalence of ESBL-KP and ESBL genes in Nigeria. Methods: A quantitative method (Meta-analysis) design was used to summarize pooled results of primary studies. Different databases [Google Scholar, PubMed, and African Journal Online (AJOL)] were searched for relevant studies. Meta-analysis was done using random-effects model. I2 and Egger test was used to ascertain heterogeneity and publication bias evaluation. Results: Eighteen observational studies were selected and the pooled prevalence of ESBL-KP in Nigeria was 47.3% [95% confidence interval (CI) 37 – 58%]. Among the genes encoding ESBL, OXA had the highest pooled prevalence in the selected studies [57% (95% CI 32, 76)], followed by TEM [55% (95% CI 36, 70)], CTX-M [54% (95% CI 38, 70)], and 41% (95% CI 27, 57). Heterogeneity tests (I2) was observed to be between 69.22 and 95.63 % for ESBL-KP and ESBL genes in the studies. Egger tests showed no publication bias (0.09 – 0.99). Conclusions: This meta-analysis demonstrated that the prevalence of ESBL-KP is increasing in Nigeria. Hence, antimicrobial stewardship and infection control measures for the prevention and spread of these strains be implemented. Keywords: Extended spectrum beta-latamase; Klebsiella Pneumonia; meta-analysis; Nigeria.

Prevalence of bacteremia and antimicrobial resistance pattern among patients in South Lebanon

Bacteremia is a leading cause of morbidity and mortality worldwide. Rising prevalence and antimicrobial resistance (AMR) are critical public health issues. This study aims to determine the prevalence of bacteremia and the AMR pattern among patients in South Lebanon. A cross-sectional study analyzed 76 positive blood cultures from Hammoud and Labib Hospitals in South Lebanon between September 2023 and March 2024. The phenotype and antimicrobial susceptibility of gram-positive and gram-negative were determined by using disk diffusion. Genotypically, polymerase chain reaction was used to detect the carbapenemase-resistant Enterobacterales (CRE), extended-spectrum β-lactamases (ESBL), and methicillin-resistant Staphylococcus aureus genes. Out of 76 isolates, 38 (50%) were gram-positive and 38 (50%) were gram-negative. Escherichia coli was the most common among gram-negative (18. 42%), with 10.52% ESBL and 3.94% CRE. Staphylococcus coagulase negative was the most common among gram-positive (40.78%), followed by Staphylococcus aureus (6.57%), with 3.94% methicillin-resistant S. aureus. The prevalent ESBL gene was CTX-M (100%), and for the CRE, NDM (66.66%) was the most common gene. Regarding S. aureus, 66.66% were mecA. The diverse bacteremia isolates and resistance genes in South Lebanon reflect global variability in incidence and resistance profiles. High rates of bacteremia and AMR in South Lebanon underscore the need for effective antibiotic stewardship programs.

Molecular characterization of blaTEM and blaCTX-M ESBLs genes producing Escherichia coli isolates from urinary tract infections (UTIs) in Al-Basrah province, Iraq

Urinary tract infections (UTIs) are primarily caused by Gram-negative Enterobacteriaceae bacteria, accounting for 80–90% of uropathogenic Escherichia coli infections. Multidrug-resistant (MDR) bacteria, such as extended-spectrum β-lactamases (ESBLS), pose a significant threat to global healthcare systems. The current study relied on 200 urine samples collected from patients suffering urinary tract infections (UTIs) in Al Sadr Teaching Hospital in Al-Basrah Province,Iraq from the 5th January to 22nd February. A result of cultivated 200 samples collected from urinary tract infection patients showed 71 (35.5%) positive samples on MacConkey agar, eosin methylene blue (EMB), and HiChromeTM E.coli agar, and bacterial growth was distributed to 47 (66.2%) Escherichia coli and 24 (33.8%) of Gram-negative species. The diagnostic gene 16S rDNA by PCR method showed that all 47 E. coli isolates had a molecular weight of around 585 bp at 100%. Furthermore, positive results were shown in 44 (93.6%) of the E.coli isolates in the current study that produced ESBLs by using the double-disc approximation method (DAM). While 3 (6.4%) isolates revealed negative results for ESBLs, whereas the13(27.7%) of the E.coli isolates gave positive results for ESBL. While 34(72.3%) E.coli isolates showed negative results for produced ESBLs by using the double-disc synergy test (DDST), there were significant differences (P<0.01) between positive and negative isolates in both methods used to detect ESBL-producing isolates. Extended-spectrum β-lactamses (ESBLs) genes were detected by using PCR to amplify the blaTEM and blaCTX-M genes in E.coli isolates. The amplified genes' bands were characterised approximately at (800 bp) for blaTEM and (754 bp) for blaCTX-M , the products were compared to the standard molecular DNA ladder at (2000 bp). According to the results, 47(100%) E.coli isolates gave positive results for the blaTEM gene. While blaCTX-M gene was shown, only 23(48.9%) E.coli isolates had positive results for the blaCTX-M gene.

Prevalence, antimicrobial resistance, and genomic characterization of Salmonella strains isolated in Hangzhou, China: a two-year study.

This study explored the molecular epidemiology and resistance mechanisms of 271 non-duplicate Salmonella enterica (S. enterica) strains, isolated mainly from adults (209/271) in a tertiary hospital in Hangzhou between 2020 and 2021. Through whole-genome sequencing and bioinformatics, the bacterial strains were classified into 46 serotypes and 54 sequence types (ST), with S. Enteritidis, S. 1,4,[5],12:i:-, and S. Typhimurium being the most prevalent serotypes and ST11, ST34, and ST19 the most common STs. The strains isolated from adults were primarily S. Enteritidis (59/209), while from children were mainly S. 1,4,[5],12:i:- (20/62). Worryingly, 12.55% strains were multi-drug resistant (MDR), with resistance rates to cefepime (FEP), ceftazidime (CAZ), ceftriaxone (CRO) and cefotaxime (CTX) of 7.38%, 9.23%, 15.87% and 16.24%, respectively, and resistance rates to levofloxacin (LEV) and ciprofloxacin (CIP) of 8.49% and 19.19%, respectively. It is worth noting that the resistance rates of CRO and CTX in children reached 30.65%. A total of 34 strains carried extended-spectrum β-lactamase (ESBL) genes, dominated by blaCTX-M-65 (13/34) and blaCTX-M-55 (12/34); it is notable that one strain of S. Saintpaul carried both blaCTX-M-27 and blaCTX-M-55. The resistance mechanism to cephalosporins was mainly due to ESBL genes (20/43), and other genes included AmpC and β-lactamase genes. The strains resistant to quinolones mainly carried qnrS1 (27/53), and others included qnrB6, aac(6')-Ib-cr, and mutations in gyrA and parC. One strain did not carry common quinolone resistance genes but had a parC (p.T57S) mutation to cause CIP resistance. This research provides vital insights into the molecular epidemiology and resistance mechanisms of clinical S. enterica, implicating possible infection control strategies.

Phenotypic antimicrobial resistance associated with different <em>bla</em> genotypes and their combinations in Enterobacterales

Introduction: Varying combinations of β-lactamase genes (bla) in Enterobacterales manifest different resistant phenotypes.Objectives: This study aimed to identify bla gene types and combinations resulting in variations in phenotypic antimicrobial resistance.Methods: Minimum inhibitory concentrations (MICs) of 75 extended spectrum β-lactamase (ESBL), AmpC β-lactamase and carbapenemase-producing Entero-bacterales isolates from a variety of clinical specimens were determined by Vitek micro-broth dilution. Bla genes were detected by 16-plex tandem PCR panel and Xpert Carba-R assay. BlaCTX-M group-1 and blaOXA-48 were the most common ESBL and carbapenemase genes, respectively.Results: Majority of the isolates (92%, 69/75) had bla gene combinations. Thirty-eight isolates (51%) carried ESBL, AmpC genes and/or narrow spectrum bla genes without any carbapenemase genes. The common bla gene combination in these isolates was blaCTX-M group-1 + blaOXA1 which is known to confer decreased susce-ptibility to piperacillin-tazobactam. Antibiotics with potential activity against ESBL-producing bacteria such as fourth generation cephalosporins, β-lactam/β-lactam-inhibitor combinations, quinolones and gentamicin also showed low rates of susceptibility. Highest susceptibility rates were to meropenem (92%) and amikacin (92%). Thirty-seven isolates (49%) carried carbapenemase genes as well. These isolates showed even higher resistance rates to all antibiotics, except amikacin (92%susceptible). Significantly higher MIC values for cefoxitin, ceftazidime, ceftriaxone, cefepime, meropenem, amikacin, tobramycin and trimethoprim-sulfamethoxazole were seen in isolates carrying blaNDM than blaOXA-48. However, a higher MIC for norfloxacin was seen in isolates with blaOXA-48.Conclusions: In conclusion, this study showed that Enterobacterales with different bla gene combinations manifest variations in phenotypic resistance to both β-lactam and non-β-lactam antibiotics.

Easy analysis of bacterial whole-genome sequencing data for clinical microbiologists using open-source Galaxy platform: Characterization of ESBL-producing Enterobacterales from bloodstream infections

ObjectivesClinical microbiologists require easy-to-use open access tools with graphical interfaces to perform bacterial whole-genome sequencing (WGS) in routine practice. This study aimed to build a bioinformatics pipeline on the open-source Galaxy platform, facilitating comprehensive and reproducible analysis of bacterial WGS data in a few steps. We then used it to characterize our local epidemiology of ESBL-producing Enterobacterales isolated from patients with bacteremia. MethodsWe built a bioinformatics pipeline consisting of the following sequential tools: Fastp (input data trimming); FastQC (read quality control); SPAdes (genome assembly); Quast (quality control of genome assembly); Prokka (gene annotation); Staramr (ResFinder database) and ABRicate (CARD database) for antimicrobial resistance (AMR) gene screening and molecular strain typing. Paired-end short read WGS data from all ESBL-producing Enterobacterales strains isolated from patients with bacteremia over one year were analysed. ResultsThe Galaxy platform does not require command line tools. The bioinformatics pipeline was constructed within one hour. It only required uploading fastq files and facilitated systematization of de novo assembly of genomes, MLST typing, and AMR gene screening in one step. Among the 66 ESBL-producing strains analysed, the two most frequent ESBL genes were blaCTX−M-15 (62.1%) and blaCTX−M-27 (13.6%). ConclusionsThe open-access Galaxy platform provides a graphical interface and easy-to-use tools suitable for routine use in clinical microbiology laboratories without bioinformatics specialists. We believe that this platform will facilitate fast and low-cost analysis of bacterial WGS data, especially in resource-limited settings.

One decade of point-prevalence surveys for carriage of extended-spectrum beta-lactamase-producing enterobacterales: whole genome sequencing based prevalence and genetic characterization in a large Dutch teaching hospital from 2013 to 2022

ObjectivesTo determine the prevalence, trends, and potential nosocomial transmission events of the hidden reservoir of rectal carriage of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E).MethodsFrom 2013 to 2022, yearly point prevalence surveys were conducted in a large Dutch teaching hospital. On the day of the survey, all admitted patients were screened for ESBL-E rectal carriage using peri-anal swabs and a consistent and sensitive selective culturing method. All Enterobacterales phenotypically suspected of ESBL production were analysed using whole genome sequencing for ESBL gene detection and clonal relatedness analysis.ResultsOn average, the ESBL-E prevalence was 4.6% (188/4,119 patients), ranging from 2.1 to 6.6% per year. The ESBL-prevalence decreased on average 5.5% per year. After time trend correction, the prevalence in 2016 and 2020 was lower compared to the other year. Among the ESBL-E, Escherichia coli (80%) and CTX-M genes (85%) predominated. Potential nosocomial transmission events could be found in 5.9% (11/188) of the ESBL-E carriers.ConclusionsThe ESBL-E rectal carriage prevalence among hospitalized patients was 4.6% with a downward trend from 2013 to 2022. The decrease in ESBL-E prevalence in 2020 could have been due to the COVID-19 pandemic and subsequent countrywide measures as no nosocomial transmission events were detected in 2020. However, the persistently low ESBL-E prevalences in 2021 and 2022 suggest that the decline in ESBL-E prevalence goes beyond the COVID-19 pandemic, indicating that overall ESBL-E carriage rates are declining over time. Continuous monitoring of ESBL-E prevalence and transmission rates can aid infection control policy to keep antibiotic resistance rates in hospitals low.

Antimicrobial Susceptibility of Commensal Escherichia coli from Pig Fecal Samples and Enhanced Sensitivity for Direct Detection of the blaCTX-M Gene by Nested PCR.

The commensal Escherichia coli in the gut of pigs is a major reservoir of antimicrobial resistance and can result in possible transmission to humans through the food chain. Direct detection of E. coli from fecal samples is challenging and can be used as a bioindicator of antimicrobial resistance. This study aimed to compare the antimicrobial susceptibility profiles in commensal E. coli from antibiotic- and nonantibiotic-using pig farms and developed the direct detection of ESBL genes in pig fecal samples using nested PCR (nPCR) and multiplex PCR (mPCR) techniques. All direct genotypic results were validated with the results of PCR sequencing of isolated E. coli colonies. The ESBL-producing E. coli were found in 98.6% (145 isolates) and 96.6% (144 isolates) of antibiotic-using and nonantibiotic-using farms, respectively, predominantly CTX-M-55. The nPCR decreased the limit of detection (LOD) from sPCR about 100 times, and the lower LODs of 102, 101, and 1 CFU/mL were reached after incubating samples in an enrichment medium for 2, 4, and 8 h, respectively. The mPCR, sPCR, and nPCR techniques showed sensitivities of 30.15%, 69.85%, and 91.91%, respectively, compared to PCR sequencing. The stability and recycling of ESBL genes were independent of antibiotic usage in commensal E. coli originating in pig farms.

Extended-spectrum β-lactamase-producing Escherichia coli from poultry: A review.

Extended-spectrum β-lactamases (ESBLs) are β-lactamase enzymes produced by Gram-negative bacterial pathogens that harbor the ESBL genes. In addition, most ESBL genes are plasmid-mediated and usually encode a broader spectrum of antimicrobial resistance, especially to penicillins, first-generation, second-generation, and third-generation cephalosporins, as well as monobactam, such as aztreonam. Escherichia coli has become an opportunistic pathogen, especially in poultry, and has been implicated in zoonotic diseases that can be transmitted to humans, resulting in public health problems. Poultry can act as carriers of ESBL-producing E. coli (ESBL-EC) bacteria to humans through poultry meat that is contaminated by waste products, feces, and excretions. The ESBL gene CTX-M type was identified as the main cause of infection in humans and was detected in poultry as a cause of infection accompanied by clinical symptoms. Several studies have also shown a link between E. coli and ESBL gene transfer from birds to humans. Controlling the spread of ESBL-EC involves maintaining the cleanliness of poultry products, especially meat, and eliminating contaminant sources from poultry. Likewise, maintaining the environmental cleanliness of poultry slaughterhouses and poultry farms must be taken as a precautionary measure to curtail the increasing spread of ESBL-EC into the environment. This review aimed to explain the spread of ESBL-producing E. coli in poultry.

Characterizing the bacteriophage PKp-V1 as a potential treatment for ESBL-producing hypervirulent K1 Klebsiella pneumoniae ST258 isolated from veterinary specimens.

The dearth of new antibiotics necessitates alternative approaches for managing infections caused by resistant superbugs. This study aimed to evaluate the lytic potential of the purified bacteriophage PKp-V1 against extended-spectrum β-lactamase (ESBL) harboring hypervirulent Klebsiella pneumoniae (hvKp)-K1 recovered from veterinary specimens. A total of 50 samples were collected from various veterinary specimens to isolate K. pneumoniae, followed by antimicrobial susceptibility testing and molecular detection of various virulence and ESBL genes. Multilocus sequence typing of the isolates was performed to identify prevalent sequence types. The bacteriophages were isolated using the double-agar overlay method and characterized using transmission electron microscopy, spot tests, plaque assays, stability tests, and one-step growth curve assays. Among 17 (34%) confirmed K. pneumoniae isolates, 6 (35%) were hvKp, whereas 13 (76%) isolates belonging to the K1 type were positive for the wzy (K1) virulence gene. All (100%) hvKp isolates exhibited the allelic profile of ST258. Overall, PKp-V1 exhibited an 88 % (15/17; (p ≤ 0.05) host range, among which all (100 %; p ≤ 0.01) hvKp isolates were susceptible to PKp-V1. PKp-V1 exhibited a lytic phage titer of 2.4 × 108 plaque forming unit (PFU)/mL at temperatures ranging from 25°C to 37°C. The lytic phage titers of PKp-V1 at pH = 8 and 0.5% chloroform were 2.1 × 108 PFU/mL and 7.2 × 109 PFU/mL, respectively. Although the incidence of ESBL-infected K. pneumoniae in veterinary settings is worrisome, PKp-V1 phages showed considerable lytic action against the host bacterium, indicating the potential of PKp-V1 as a possible alternative therapeutic option against MDR K. pneumoniae.

Prevalence of plasmid-mediated quinolone resistance genes in extended-spectrum beta-lactamase producing Klebsiella pneumoniae isolates in northern Iran

Plasmid-mediated quinolone resistance (PMQR) in extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae (K. pneumoniae) contributes to treatment failures, extended hospital stays, and increased mortality percentages. We aimed to determine the prevalence of PMQR genes in ESBL-producing K. pneumoniae isolates from clinical samples in Babol, North of Iran region. This is the first study in this region to investigate this specific association. A total of 95 K. pneumoniae isolates were obtained from hospitalized patients with various clinical infections during March 2022 to February 2023. Disk diffusion and Combination disk method were performed to identification of antimicrobial resistance profiles and ESBL-producing strains. The presence of ESBL and PMQR genes among K. pneumoniae isolates was assessed using polymerase chain reaction (PCR) method. Of the isolates, 68 (71.57 %) were considered as ESBL-producers. The blaTEM, blaSHV and blaCTX-M genes were detected in 74.73 %, 57.89 %, and 41.05 % of K. pneumoniae isolates, respectively. Among the PMQR encoding genes, the highest and lowest frequency was associated to qepA (67.3 %) and qnrA (4.2 %), respectively. The frequency of qnrA, qnrB, qnrS, acc (6′)-Ib-cr, qepA, oqxA, and oqxB genes in 26 MDR-Kp isolates was 11.53 % (n; 3), 69.23 % (n; 18), 65.38 % (n; 17), 73.07 % (n; 19), 80.76 % (n; 21), 84.61 % (n; 22), and 76.92 % (n; 20), respectively. Our result revealed of the 68 ESBL gene-positive isolates, 60 (88.23 %) were positive for the PMQR gene. The co-occurrence of these genes within resistant isolates suggests potential linkage on mobile genetic elements such as plasmids. These findings highlight the significant burden of PMQR determinants in ESBL-producing K. pneumoniae and underscore the urgent need for effective control measures. Implementing robust antimicrobial stewardship programs and strengthening drug-resistance surveillance and control protocols are crucial to prevent the spread of resistant isolates.

Dynamics of antimicrobial resistance and genomic characteristics of foodborne Vibrio spp. in Southern China (2013–2022)

Vibrio spp., known as significant marine pathogens, have become more prevalent due to global warming. Antibiotics released into the environment drive Vibrio resistance. The increasing consumption of seafood leads to more interactions between Vibrio and humans. Despite this concerning trend, there remains a lack of large-scale surveillance for Vibrio contamination across various types of food. This study isolated 4027 Vibrio strains, primarily comprising V. parahaemolyticus and V. alginolyticus, in 3581 fresh shrimp and meat products from 2013 to 2022. The Vibrio strains showed increased resistance to important antibiotics, especially β-lactams used to treat foodborne bacterial infections. Whole genome sequencing of 591 randomly chosen strains showed a strong correlation between antibiotic resistance and genotypes in Vibrio. Notably, various ESBL genes have evolved over the past 8 years, with blaVEBs being the most dominant. Additionally, carbapenemase genes, such as blaNDM-1, have become increasingly prevalent in recent years. Various mobile genetic elements, including IncQ and IncA/C plasmids, recoverable in Vibrio, facilitate the transmission of crucial β-lactamase genes. These data provide insights into the evolutionary traits of antimicrobial resistance in foodborne Vibrio strains over a decade. Policymakers should consider these findings when devising appropriate strategies to combat bacterial antimicrobial resistance and safeguard human health.

Distribution and Antimicrobial Resistance of Complicated Intraabdominal Infection Pathogens in Two Tertiary Hospitals in Egypt.

Background: Management of complicated intraabdominal infections (cIAIs) requires containment of the source and appropriate initial antimicrobial therapy. Identifying the local data is important to guide the empirical selection of antimicrobial therapy. In this study, we aimed to describe the pathogen distribution and antimicrobial resistance of cIAI. Methods: In two major tertiary care hospitals in Egypt, we enrolled patients who met the case definition of cIAI from October 2022 to September 2023. Blood cultures were performed using the BACTAlert system (BioMerieux, Marcy l'Etoile, France). A culture of aspirated fluid, resected material, or debridement of the infection site was performed. Identification of pathogens and antimicrobial susceptibility testing were conducted by the VITEK-2 system (BioMerieux, Marcy l'Etoile, France). Gram-negative resistance genes were identified by PCR and confirmed by whole bacterial genome sequencing using the Nextera XT DNA Library Preparation Kit and sequencing with the MiSeq Reagent Kit 600 v3 (Illumina, USA) on the Illumina MiSeq. Results: We enrolled 423 patients, 275 (65.01%) males. The median age was 61.35 (range 25-72 years). We studied 452 recovered bacterial isolates. Gram-negative bacteria were the vast majority, dominated by E. coli, followed by Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, and Proteus mirabilis (33.6%, 30.5%, 13.7%, 13%, and 5.4%, respectively). High rates of resistance were detected to third- and fourth-generation cephalosporins and fluoroquinolones. No resistance was detected to colistin. Resistance to amikacin and tigecycline was low among all isolates. Resistance to meropenem and ceftazidime/avibactam was moderate. ESBL genes were common in E. coli and K. pneumoniae. CTX-M15 gene was the most frequent. Among Enterobacterales, blaOXA-48 and blaNDM were the most prevalent carbapenemase genes. Pseudomonas aeruginosa isolates harbored a wide variety of carbapenemase genes (OXA, NDM, VIM, SIM, GIM, SPM, IMP, AIM), dominated by metallo-beta-lactamases. In 20.6% of isolates, we identified two or more resistance genes. Conclusion: High resistance rates were detected to third- and fourth-generation cephalosporins and fluoroquinolones. Amikacin and tigecyclines were the most active antimicrobials. Our data call for urgent implementation of antimicrobial stewardship programs and reinforcement of infection control.