Antimicrobial Resistance and Molecular Epidemiology of ESBL-Producing Escherichia coli Isolated from Outpatients in Town Hospitals of Shandong Province, China

Tracking spatio-temporal distribution and transmission of antibiotic resistance in aquatic environments by using ESBL-producing Escherichia coli as an indicator

Wastewater treatment plants (WWTPs) play an important role in the production, and transmission of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) as a convergence for human, animal, and environmental wastewater. The aim of this study was to investigate the spatio-temporal variation and influencing factors of ARB in different functional areas of the urban WWTP and the connecting rivers for 1-year monitoring using extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) as an indicator bacteria, and to study the transmission patterns of ARB in the aquatic environment. The results showed that ESBL-Ec isolates were identified from the WWTP (n = 219), including influent (n = 53), anaerobiotic tank (n = 40), aerobiotic tank (n = 36), activated sludge tank (n = 31), sludge thickner tank (n = 30), effluent (n = 16), and mudcake storage area (n = 13). The dehydration process can significantly remove the ESBL-Ec isolates; however, ESBL-Ec was still detected in samples collected from the effluent of the WWTP (37.0%). The detection rate of ESBL-Ec was significantly different across seasons (P < 0.05), and ambient temperature was negatively correlated with the detection rate of ESBL-Ec (P < 0.05). Furthermore, a high prevalence of ESBL-Ec isolates (29/187, 15.5%) was detected in samples collected from the river system. These findings emphasize that the high majority of ESBL-Ec in aquatic environments is alarming because it poses a significant threat to public health. Clonal transmission of ESBL-Ec isolates between the WWTP and rivers based on the spatio-temporal scale was observed by pulsed-field gel electrophoresis analysis, ST38 and ST69 ESBL-Ec clone were selected as prioritized isolates for antibiotic resistance monitoring in the aquatic environment. Further phylogenetic analysis showed human-associated (feces, blood) E. coli was the main source contributing to the presence of antibiotic resistance in aquatic environments. Longitudinal and targeted monitoring of ESBL-Ec in WWTPs and the development of effective wastewater disinfection strategies before effluent discharge from WWTPs are urgently required, to prevent and control the spread of antibiotic resistance in the environment.

Emergence of ST1193 Clone in Maternal and Neonatal ESBL-Producing E. coli Isolates

Objective

The emerging epidemic of extended-spectrum β-lactamase-producing E. coli (ESBL-EC) is a global public health crisis. ESBL-EC infections are increasing worldwide and contribute to morbidity and mortality among newborn infants. However, the antimicrobial resistance characteristics and clonal transmission of maternal and neonatal ESBL-EC isolates need to be further deciphered.

Materials and Methods

We performed phenotypic and genotypic characterization of 33 ESBL-EC isolates from pregnant women and newborn during 2019-2020.

Results

Minimum inhibitory concentrations of 17 antimicrobial agents showed that all isolates were multidrug-resistant (MDR) and had a resistance rate of 100% to ampicillin, and mild resistance to florfenicol, gentamicin, ceftazidime, and amoxicillin-clavulanate. Additionally, imipenem, meropenem, polymyxin, and tigecycline exhibited good activity against the tested ESBL-EC isolates with low MIC50 (0.06-1 μg/mL) and MIC90 (0.06-1 μg/mL). Whole genome sequencing indicated that ESBL-EC isolates contained diverse antimicrobial resistant genes (blaCTX-M, blaTEM, blaSHV, tetA, etc.) and toxin genes (ompA, csg, fimH, hybtA, etc.). blaCTX-M genes were the main ESBL genotype. ST1193 (18.2%) was the second most abundant ST among the ESBL-EC isolates (ST131 was the most common, with 30.3%), and this is the first report of its mother-to-infant colonization transmission in China.

Conclusion

These findings revealed the occurrence of high-risk ST1193 clone among ESBL-EC isolates from pregnant women and newborn colonization in China. Further national or regional multicenter studies are needed to assess the dissemination and evolution of ESBL-EC ST1193 clone as a nosocomial pathogen in China.

Implications of different waterfowl farming on cephalosporin resistance: Investigating the role of blaCTX-M-55

We investigated the cephalosporin resistance of Escherichia coli from waterfowl among different breeding mode farms. In 2021, we isolated 200 strains of E. coli from waterfowl feces samples collected from Sichuan, Heilongjiang, and Anhui provinces. The key findings are: Out of the 200 strains, 80, 80, and 40 strains were isolated from waterfowl feces samples in intensive, courtyard, and outdoor breeding mode farms, respectively. The overall positive rate of the ESBL phenotype, detecting by the double disk diffusion method, was 68.00% (136/200). In particular, the rates for intensive, courtyard, and outdoor breeding modes were 98.75%, 36.25%, and 70.00%, respectively. Results of MIC test showed drug resistance rates in the intensive breeding mode: 100.00% for cephalothin, 38.75% for cefoxitin, 100.00% for cefotaxime, and 100.00% for cefepime. In courtyard breeding mode, the corresponding rates were 100.00%, 40.00%, 63.75%, and 45.00%, respectively. In outdoor breeding mode, the corresponding rates were 100.00%, 52.50%, 82.50%, and 77.50%, respectively. The PCR results for blaCTX-M, blaTEM, blaOXA, and blaSHV showed the detection rate of blaCTX-M was highest at 75.50%, with blaCTX-M-55 is the main subtype gene, followed by blaTEM at 73.50%. We screened 58 donor strains carrying blaCTX-M-55, including 52 strains from the intensive breeding mode. These donor bacteria can transfer different plasmids to recipient E. coli J53, resulting in recipient bacteria acquiring cephalosporin resistance, and the conjugational transfer frequency ranged from 1.01 × 10-5 to 6.56 × 10-2. The transferred plasmids remained stable in recipient bacteria for up to several days without significant adaptation costs observed. During molecular typing of E. coli with conjugational transfer ability, the blaCTX-M-55 was found to be widely present in different ST strains with several phylogenetic groups. In summary, cephalosporin resistance of E. coli carried by waterfowl birds in intensive breeding mode farm was significantly higher than in courtyard and outdoor mode farms. The blaCTX-M-55 subtype gene was the prevalent ARGs and can be horizontally transferred through plasmids, which plays a key role in the spread of cephalosporin drug resistance.

Antimicrobial Resistance Profile by Metagenomic and Metatranscriptomic Approach in Clinical Practice: Opportunity and Challenge

The burden of bacterial resistance to antibiotics affects several key sectors in the world, including healthcare, the government, and the economic sector. Resistant bacterial infection is associated with prolonged hospital stays, direct costs, and costs due to loss of productivity, which will cause policy makers to adjust their policies. Current widely performed procedures for the identification of antibiotic-resistant bacteria rely on culture-based methodology. However, some resistance determinants, such as free-floating DNA of resistance genes, are outside the bacterial genome, which could be potentially transferred under antibiotic exposure. Metagenomic and metatranscriptomic approaches to profiling antibiotic resistance offer several advantages to overcome the limitations of the culture-based approach. These methodologies enhance the probability of detecting resistance determinant genes inside and outside the bacterial genome and novel resistance genes yet pose inherent challenges in availability, validity, expert usability, and cost. Despite these challenges, such molecular-based and bioinformatics technologies offer an exquisite advantage in improving clinicians’ diagnoses and the management of resistant infectious diseases in humans. This review provides a comprehensive overview of next-generation sequencing technologies, metagenomics, and metatranscriptomics in assessing antimicrobial resistance profiles.

Antimicrobial Resistance and Molecular Epidemiology of Escherichia coli From Bloodstream Infection in Shanghai, China, 2016-2019

Background: Bloodstream infections are recognized as important nosocomial infections. Escherichia coli (E. coli) is the most prevalent Gram-negative bacillary pathogen causing bloodstream infections (BSIs). This retrospective study investigated drug susceptibility and molecular epidemiology of E. coli isolated from patients with BSI in Shanghai, China.

Methods: We collected E. coli isolated from the blood cultures of patients with BSI between January 2016 and December 2019. We randomly selected 20 strains each year to investigate antimicrobial resistance, resistance genes, and molecular epidemiological characteristics. Antimicrobial susceptibility testing was performed by the disk diffusion method. PCR was performed to detect extended-spectrum β-lactamases (ESBLs), carbapenemase genes, and housekeeping genes, and phyloviz was applied to analyze multilocus sequence typing (MLST).

Results: Penicillins, first- and second-generation cephalosporins and fluoroquinolones have high resistance rates (>60%). Among the 80 randomly selected strains, 47 (58.8%) produced ESBLs, and one produced carbapenemase. Sequencing of resistance genes identified bla_CTX−M−14 (34%, 16/47), bla_CTX−M−15 (23.4%, 11/47) and bla_CTX−M−27 (14.8%, 7/47) as the most prevalent genotypes of ESBLs. ST131 (14/80) was the most prevalent sequence type (ST), followed by ST1193 (10/80), ST648 (7/80).

Conclusions: Our findings suggest that amikacin, carbapenems, and piperacillin-tazobactam have relatively low resistance rates and may be the preferred antibiotic regimens for empiric therapy. ST131 and bla_CTX−M−14 are still the main prevalent in Shanghai with a rapid increase in the occurrence of ST1193 is rapidly increasing and more diverse bla_CTX genes.

Coexistence of virulence and β-lactamase genes in avian pathogenic Escherichia coli

Emergence of multidrug resistance in E. coli and advent of newer strains is becoming serious concern which requires keen observations. This study was designed to find the ciprofloxacin resistant E. coli isolates co-existed with multi-drug resistance along with β-lactamase production from poultry source, and finally the genome sequencing of these strains to explore genetic variations. Study constituted on isolation of n = 225 E. coli from broiler farms of central China which were further subjected to identification of resistance against ciprofloxacin followed by antibiogram of n = 26 antibiotics and identification of β-lactamase production. Whole genome resequencing was performed using Illumina HiSeq 4000 system. PCR results revealed predominant β-lactamase genes i.e.CTX-M, CTX-M-1, CTX-M3, TEM-1 and OXA. Furthermore, the MDR isolates were containing most of the tested virulence genes. The most prevalent virulence genes were pap-C, fim-C, fim-H, iuc-D, irp-2, tra-T, iro-N and iut-A. The single nucleotide polymorphisms (SNPs) loci mentioned in this data give valuable genetic markers to growing high-throughput techniques for fine-determination of genotyping of MDR and virulent isolates. Characterization of SNPs on functional basis shed new bits of knowledge on the evolution, disease transmission and pathogenesis of MDR E. coli isolates. In conclusion, these findings provide evidence that most of poultry E. coli are MDR, β-lactamase producers, and virulent which could be a zoonotic threat to the humans. The whole genome resequencing data provide higher resolution of resistance and virulence characteristics in E. coli which can further be used for the development of prevention and treatment strategies.

Prevalence, detection and characterisation of fosfomycin-resistant Escherichia coli strains carrying fosA genes in Community of Madrid, Spain

OBJECTIVES

The aim of this this study was to describe the presence of different variants of the fosA gene in fosfomycin-resistant Escherichia coli strains in Madrid, Spain.

METHODS

fos genes were searched for in 55 E. coli strains collected from seven representative hospitals located in Madrid. A phenotypic screening test was performed following the disk diffusion method with sodium phosphonoformate added as described by Nakamura et al. Additionally, a molecular study based on PCR was used to confirm the screening results. Positive strains for fos genes were further subjected to whole-genome sequencing (WGS).

RESULTS

Phenotypic screening was positive in 9/55 strains (16.4%), although genotypic detection was positive in only 3 (fosA3, fosA4 and fosA6). Thus, the prevalence of fos genes in Madrid was 5.5% (3/55). WGS data were not available for the fosA6-positive strain. One isolate with fosA3 (ST69) carried a bla_CTX-M-55 gene and seven virulence genes (air, eilA, iha, iss, lpfA, sat and senB). The fosA4-positive isolate (ST4038) carried the virulence genes iss, lpfA, iroN and mchF. Both fos genes were located between two IS26 mobile elements of a plasmid.

CONCLUSION

We detected the presence of different variants of plasmid-mediated fosA genes in fosfomycin-resistant E. coli strains in Madrid, Spain. Despite the few reports in Europe, it would be of interest to monitor the spread of these acquired resistance genes.

Molecular detection of extended spectrum β-lactamase genes in Escherichia coli clinical isolates from diarrhoeic children in Kano, Nigeria

The increase in antimicrobial resistance in developed and developing countries is a global public health challenge. In this context β-lactamase production is a major contributing factor to resistance globally. The aim of this study was to determine the prevalence of phenotypic and genotypic extended spectrum β-lactamases (ESBLs) in 296 E. coli isolates recovered from diarrhoeic children younger than five years in Kano whose susceptibility profile against 7 antimicrobials had been determined. The E. coli isolates were subjected to double disc synergy test for phenotypic ESBLs detection and ESBL associated genes (bla_CTX-M, bla_TEM and bla_SHV) were detected using conventional PCR. Phenotypically, 12.8% (38/296) E. coli isolates presented a ESBLs phenotype, with a significantly higher proportion in isolates from females compared with males (P-value = 0.024). bla_CTX-M 73.3% and bla_TEM 73.3% were the predominant resistance genes in the ESBLs positive E. coli (each detected in 22/30 isolates, of which 14 harboured both). In addition, 1/30 harboured bla_CTX-M + bla_TEM + bla_SHV genes simultaneously. This study demonstrates the presence of ESBLs E. coli isolates in clinically affected children in Kano, and demonstrates the circulation of bla_CTX-M and bla_TEM associated with those phenotypes. Enactment of laws on prudent antibiotic use is urgently needed in Kano.

Antimicrobial Resistance in Agri-Food Chain and Companion Animals as a Re-emerging Menace in Post-COVID Epoch: Low-and Middle-Income Countries Perspective and Mitigation Strategies

Antimicrobial resistance (AMR) leads to enormous financial losses from issues such as high morbidity, mortality, man-days lost, hospital length of stay, health-care, and social costs. In humans, over prescription of antimicrobials, which is presumably higher during COVID, has been identified as the major source of selection for antimicrobial resistant bacteria; however, use of antimicrobials in food and companion animals, fish, and vegetables, and the environmental resistance gene pool, also play important roles. The possibilities of unnecessary use of antibiotics as prophylaxis during and after COVID in livestock and companion animals exist in low-and middle-income countries. A considerable loss in gross domestic product (GDP) is also projected in low-and middle-income countries (LMICs) due to AMR by the year 2050, which is further going to be reduced due to economic slowdown in the post-COVID period. Veterinary hospitals dedicated to pets have cropped up, especially in urban areas of LMICs where use of antimicrobials has also been increased substantially. The inevitable preventive habit built up during COVID with the frequent use of hand sanitizer might trigger AMR due to the presence of cross-resistance with disinfectants. In LMICs, due to the rising demand for animal protein, industrial food animal production (IFAP) is slowly replacing the small-scale backyard farming system. The lack of stringent regulations and monitoring increased the non-therapeutic use of antimicrobials in industrial farms where the persistence of antimicrobial resistant bacteria has been associated with several factors other than antimicrobial use, such as co-resistance, cross-resistance, bacterial fitness, mixing of new and old animals, and vectors or reservoirs of bacterial infection. The present review describes types of antimicrobials used in agri-food chains and companion animals in LMICs with identification of the gap in data, updated categories of prevalent antimicrobial resistant bacteria, the role of animal farms as reservoirs of resistant bacteria, and mitigation strategies, with a special focus on the pivotal strategy needed in the post-COVID period.

CTX-M type extended-spectrum β-lactamase in Escherichia coli isolated from extra-intestinal infections in a tertiary care hospital in south India

Background & objectives:

Infections caused by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli carrying bla_CTX-M genes have been spreading globally, but there are geographical variations in the type of bla_CTX-M genes prevalent and there are scanty data from India. This study was conducted to determine the CTX-M type ESBLs in E. coli isolates obtained from clinical specimens from patients with extra-intestinal infections attending a tertiary care hospital in south India.

Methods:

ESBL-producing E. coli isolated from patients with extra-intestinal infections were subjected to PCR using CTX-M group-specific primers. From a representative isolate, full-length CTX-M-15 gene was amplified and sequenced. An internal fragment of this gene was sequenced in 10 representative isolates.

Results:

Of the 300 isolates of E. coli tested, 88 per cent carried CTX-M genes and bla_CTX-M-15 was the most dominant gene present in 90 per cent of the positive isolates. Most (91%) of the isolates positive for bla_CTX-M were sensitive to meropenem.

Interpretation & conclusions:

Our findings showed bla_CTX-M-15 to be the dominant gene. Based on the data on antimicrobial susceptibility, cefoperazone-sulbactum could be an antimicrobial of choice.

Determination of the frequency of β-lactamase genes (bla SHV, bla TEM, bla CTX-M) and phylogenetic groups among ESBL-producing uropathogenic Escherichia coli isolated from outpatients

Background

Escherichia coli accounts for 70–95% of community-acquired urinary tract infections (UTIs). Recently, there has been an increase in the prevalence of extended-spectrum β-lactamase (ESBL) in the community which required an accurate identification for better management. Therefore, the current study was performed to determine the antimicrobial resistance pattern, investigate ESBL phenotypes and genotypes (blaCTX-M, bla TEM and bla SHV genes) and determine the phylogenetic groups among ESBL-positive isolates from outpatients.

Methods

One hundred and eighty-three positive urine samples were collected from 4450 outpatient clinic attendees. Antibiotic susceptibility was determined and ESBL phenotype screening was carried out using disk diffusion agar and combination disk techniques, respectively. The assessment of the presence of the blaCTX-M, bla TEM and blaSHV genes and phylogenetic grouping were performed using the polymerase chain reaction (PCR) method.

Results

Out of 183 E. coli isolates, 59 (32.2%) showed a positive ESBL phenotype. The prevalence of ESBL-producing E. coli was higher in males (57.4%). Fifty-seven of the ESBL-producing strains carried at least one of the β-lactamase genes (bla CTX-M, bla TEM, bla SHV). Phylotyping of multi-drug resistant isolates indicated that the isolates belonged to B2, A and D phylogroups. Analysis of resistance patterns among these phylogroups revealed that 74.4%, 55.3% and 29.7% of the isolates in the B2 group were resistant to trimethoprim-sulfamethoxazole, ciprofloxacin and gentamicin, respectively. Most of the strains in the phylogroup B2 carried the bla CTX-M gene.

Conclusions

All the ESBL-producing isolates were placed in one of the four phylogenetic groups. The presence of CTX-M and resistance to quinolones were more frequent in B2 strains than in non-B2 strains.

Metagenomics: aid to combat antimicrobial resistance in diarrhea

Antimicrobial resistance (AMR) has emerged as an obstacle in the supple administration of antimicrobial agents to critical diarrheal patients. Most diarrheal pathogens have developed resistance against the major classes of antibiotics commonly used for assuaging diarrheal symptoms. Antimicrobial resistance develops when pathogens acquire antimicrobial resistance genes (ARGs) through genetic recombination from commensals and pathogens. These are the constituents of the complex microbiota in all ecological niches. The recombination events may occur in the environment or in the gut. Containment of AMR can be achieved through a complete understanding of the complex and diverse structure and function of the microbiota. Its taxonomic entities serve as focal points for the dissemination of antimicrobial resistance genetic determinants. Molecular methods complemented with culture-based diagnostics have been historically implemented to document these natural events. However, the advent of next-generation sequencing has revolutionized the field of molecular epidemiology. It has revolutionized the method of addressing relevant problems like diagnosis and surveillance of infectious diseases and the issue of antimicrobial resistance. Metagenomics is one such next-generation technique that has proved to be a monumental advancement in the area of molecular taxonomy. Current understanding of structure, function and dysbiosis of microbiota associated with antimicrobial resistance was realized due to its conception. This review describes the major milestones achieved due to the advent and implementation of this new technique in the context of antimicrobial resistance. These achievements span a wide panorama from the discovery of novel microorganisms to invention of translational value.

Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae and urinary tract infections in pregnant/postpartum women: A systematic review and meta-analysis

BACKGROUND

Urinary tract infections (UTI) and asymptomatic bacteriuria (AB) during pregnancy can result in considerable maternal and foetal adverse outcomes. Production of extended-spectrum beta-lactamase (ESBL) is a major antibiotic resistance mechanism by Enterobacteriaceae.

OBJECTIVES

To determine the global prevalence of ESBL-producing (ESBL-P) Enterobacteriaceae in symptomatic UTI/AB among pregnant/postpartum females.

DATA SOURCES

A systematic review of the PubMed, Embase, Scopus, WOS (Web of Science), ProQuest and the grey literature was conducted.

STUDY SELECTION AND DATA EXTRACTION

Studies that reported the frequency of ESBL-P Enterobacteriaceae in pregnant/postpartum women with UTI and/or AB were eligible. First, the titles and abstracts of the retrieved articles were reviewed. Then, the full texts of the remained articles were reviewed.

SYNTHESIS

In order to estimate the pooled prevalence and the 95% confidence interval (95% CI), meta-analysis was performed using the random-effects model.

RESULTS

Twenty-three studies (six from Africa, two from North America, one from South America, 12 from Asia and two European studies) that reported data on 20 033 Enterobacteriaceae strains were included. The pooled prevalence of ESBL-P Enterobacteriaceae was 25% (95% CI 18%, 32%); I2  = 98.8%. The estimated prevalence (95% CI) rates were 45% (22, 67%) in Africa, 33% (22, 44%) in India, 15% (6, 24%) in other Asian countries, 5% (2, 8%) in Europe, 4% (1, 11%) in South America and 3% (1, 5%) in North America (P < .001). This estimate was 21% (95% CI 11, 31%) in patients with symptomatic UTI and it was 28% (95% CI 15, 41%) in patients with AB (P = .40).

CONCLUSIONS

The prevalence of ESBL-P Enterobacteriaceae among pregnant women with UTI/AB was significant and geographic region was a major source for heterogeneity. The findings could be taken into account by healthcare providers and programmers in the management and antibiotic selection of UTI/AB during pregnancy, especially in high prevalence areas.

Colonisation with extended-spectrum β-lactamase-producing Enterobacteriaceae in pregnant/post-partum women: Systematic review and meta-analysis

OBJECTIVES

Maternal colonisation with extended-spectrum β-lactamase (ESBL)-producing micro-organisms can lead to transmission of such pathogens to neonates, resulting in considerable morbidity. The aim of this study was to determine the global prevalence of maternal colonisation with ESBL-producing Enterobacteriaceae (ESBL-E).

METHODS

A systematic review of PubMed, Embase, Scopus, Web of Science and ProQuest databases as well as the grey literature was performed. Studies reporting the prevalence of ESBL-E colonisation during pregnancy or postpartum period were included. Prevalence data were grouped by geographic region. The pooled prevalence and 95% confidence interval (CI) was estimated by meta-analysis using a random-effects model.

RESULTS

Nineteen studies with reports from 16 countries (seven studies from Africa, one study from South America, two studies from Asia and nine studies from Europe) reporting data for 7352 pregnant/postpartum women were included. The pooled prevalence of ESBL-E colonisation was 8% (95% CI 5-10%). Prevalence estimates were 15% (95% CI 5-24%) in Africa, 6% (95% CI 4-10%) in South America, 5% (95% CI 4-6%) in Asia and 4% (95% CI 2-5%) in Europe. The pooled prevalence was higher in studies with low risk of bias (10%; 95% CI 7-13%) compared with those with high risk of bias (3%; 95% CI 2-3%).

CONCLUSION

There was heterogeneity regarding ESBL-E colonisation rates in different continents. The pooled prevalence rate was higher in Africa compared with other areas. Given that the highest rate was observed in Africa, implementing screening efforts for ESBL-E colonisation during pregnancy may be justified.

Human, animal and environmental contributors to antibiotic resistance in low-resource settings: integrating behavioural, epidemiological and One Health approaches

Antibiotic resistance (ABR) is recognized as a One Health challenge because of the rapid emergence and dissemination of resistant bacteria and genes among humans, animals and the environment on a global scale. However, there is a paucity of research assessing ABR contemporaneously in humans, animals and the environment in low-resource settings. This critical review seeks to identify the extent of One Health research on ABR in low- and middle-income countries (LMICs). Existing research has highlighted hotspots for environmental contamination; food-animal production systems that are likely to harbour reservoirs or promote transmission of ABR as well as high and increasing human rates of colonization with ABR commensal bacteria such as Escherichia coli However, very few studies have integrated all three components of the One Health spectrum to understand the dynamics of transmission and the prevalence of community-acquired resistance in humans and animals. Microbiological, epidemiological and social science research is needed at community and population levels across the One Health spectrum in order to fill the large gaps in knowledge of ABR in low-resource settings.

Phenotypic and genotypic characterization of multi-drug-resistant Escherichia coli isolates harboring blaCTX-M group extended-spectrum β-lactamases recovered from pediatric patients in Shenzhen, southern China

Aims and Objectives: The emergence and spread of extended-spectrum β-lactamases (ESBLs) particularly CTX-M producing multi-drug-resistant (MDR) Escherichia coli (E. coli) is one of the greatest challenges for community health globally. The study investigated the phenotypic and genotypic characteristics of ESBLs-producing E. coli recovered from pediatric patients from Shenzhen Children’s Hospital, China.

Materials and methods: Present study, a total of 2,670 isolates of E. coli were collected from Shenzhen Children’s Hospital, China of which 950 were ESBLs producer. ESBLs production was confirmed by using the combination disc diffusion method, and antimicrobial susceptibility test was detected. In addition, β-lactamase-producing genes and co-existence of carbapenem/colistin resistance genes were determined by PCR assay and sequencing. The diversity and phylogenetic relationship were determined by multi-locus sequence typing method.

Results: Thirty-five percent (n=950) prevalence of ESBLs-producing E. coli we reported in Shenzhen, China of which 50 ESBLs producing E. coli were randomly selected for a further characterization. All 50 ESBLs- producing E. coli isolates revealed MDR phenotype and 100% were resistant to Ampicillin/sulbactam, Ampicillin, Cefazolin, and Ceftriaxone. All 50 ESBLs producers harbored at least one type of β-lactamase gene particular bla_CTX-M. The PCR and sequencing revealed the most common CTX-M subtype was bla_CTX-M-15 (n=18), followed by bla_CTX-M-14 (n=16), bla_CTX-M-90 (n=9), bla_CTX-M-55 (n=3), bla_CTX-M-27, bla_CTX-M-101, and bla_CTX-M-211 each (n=1). Co-existence of bla_CTX-M with bla_TEM, bla_SHV, bla_GES, and bla_VEB was detected in few isolates. Among identified sequence types, ST131 (12%) was more dominant in ESBLs-producing E. coli. Phylogenetic group A was the most prominent group among the ESBLs-producing E. coli based on multiplex PCR.

Conclusion: Our study shows the prevalence of bla_CTX-M gene in ESBLs-producing E. coli in pediatric patients in Shenzhen, China. We highlight the importance to monitor the emergence and trends of ESBLs-producing isolates in a pediatric healthcare setting.

Detection of O25b-ST131 clone, CTX-M-1 and CTX-M-15 genes via real-time PCR in Escherichia coli strains in patients with UTIs obtained from a university hospital in Istanbul

BACKGROUND

Escherichia coli sequence type 131 is an important multidrug resistant clone responsible from more than half of ESBL-producing E.coli isolates. Aim of this study was to investigate the presence of O25b-ST131 clone, CTX-M-15 and CTX-M-1 genes in the E. coli strains isolated from both hospital and community acquired UTIs by real-time PCR and to reveal molecular epidemiological data.

METHODS

Non-duplicate E. coli (n = 101) strains isolated from UTI patients were included. Bacterial identifications were performed with VITEK Compact. Antimicrobial susceptibility tests, phenotypic ESBL and E-tests were performed conventionally. Real-time PCR was utilized to detect presence of O25b-ST131 clone, blaCTX-M-15 and blaCTX-M-1.

RESULTS

O25b-ST131 clone, CTX-M-1 and CTX-M-15 were detected in 22%, 73%, 37% in UTIs, respectively. Presence of O25b-ST131 clones and CTX-M-1 genes among E. coli strains isolated from inpatients were found statistically higher than outpatients. The most effective choice was found to be fosfomycin and nitrofurantoin in outpatients and inpatients, respectively. The MIC₉₀ values of Amikacin, Cefotaxime, Cefepime and Ciprofloxacin were higher in inpatients than in oupatients, whereas Cefotaxime and Ciprofloxacin MIC₅₀ values were found to be higher in inpatients than in outpatients. The highest increase of MIC₉₀ values was observed in O25b-ST131, CTX-M-1 and CTX-M-15 coexistence.

CONCLUSION

The presence of O25b-ST131 clone, CTX-M-1 and CTX-M-15 genes in E. coli strains in patients with UTI has been revealed. In the presence of the O25b-ST131 clone, a significant increase was observed in the ciprofloxacin MIC values indicating the importance of monitorization of the clone using molecular epidemiology.

Assessment of the Exposure of Turkey Farmers to Antimicrobial Resistance Associated with Working Practices

The objective of the present study was the identification of farming practices in the production of turkeys for human consumption, and their ranking in terms of the occupational probability of exposure to antimicrobial resistant (AMR) bacteria, for farm workers. We gathered evidence and data from scientific literature, on risk factors for AMR in farmers, and on the prevalence of those hazards across farming phases. We administered semi-structured interviews to public and private veterinarians in Northern Italy, to obtain detailed information on turkey farming phases, and on working practices. Data were then integrated into a semi-quantitative Failure Modes and Effect Analysis (FMEA). Those working practices, which are characterized by direct contact with numerous animals, and which are carried out frequently, with rare use of personal protection devices resulted as associated with the greatest probability of exposure to AMR. For methicillin resistant Staphylococcus aureus (MRSA), these included vaccination and administration of any individual therapy, and removal and milling of litter, given the exposure of farmers to high dust level. Indeed, levels of occupational exposure to MRSA are enhanced by its transmission routes, which include direct contact with animal, as well as airborne transmission. Level of exposure to extended spectrum beta lactamase (ESBL) is more strictly associated with direct contact and the oral-fecal route. Consequently, exposure to ESBL resulted and associated with the routinely tipping over of poults turned on their back, and with the individual administration of therapies.

Prevalence of extended-spectrum β-lactamase-producing Klebsiella pneumoniae: First systematic review and meta-analysis from Iran

OBJECTIVES

Extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ESBL-KP) have emerged as an important pathogen causing severe infections worldwide. Infections due to ESBL-KP are associated with high morbidity and mortality, especially in developing countries such as Iran. The aim of this study was to assess the pooled prevalence of ESBL-KP with different gene variants in Iran.

METHODS

A literature search of Medline (via PubMed), Embase, Web of Science and Iranian Database was performed. A meta-analysis was conducted using Comprehensive Meta-Analysis Software (version 2.2, Biostat). A fixed- or random-effects model was used based on the heterogeneity test. Publication bias was determined using Begg's rank correlation and Egger's weighted regression methods.

RESULTS

Among 783 articles identified, 43 studies met the eligibility criteria. The pooled prevalence of ESBL-KP was 43.5% (95% CI 39.3-47.9%) among clinical K. pneumoniae isolates. Among genes encoding ESBLs during 2000-2009, SHV, CTX-M and TEM were found with prevalences of 23.3%, 15.2% and 12.3%, respectively, whilst the prevalences of SHV, CTX-M, TEM and VEB were 24%, 28.1%, 25.2% and 8.3%, respectively, during the period 2010-2018.

CONCLUSION

The prevalence of ESBL-KP has increased steadily in recent years among clinical K. pneumoniae isolates in Iran. Thus, initial identification of ESBL-KP according to Clinical and Laboratory Standards Institute (CLSI) guidelines, proper molecular approaches, and implementation of antimicrobial stewardship programmes in Iranian hospitals together with comprehensive infection control measures are urgently needed to control the dissemination of these strains.

Phenotypic and genotypic characterizations of extended-spectrum beta-lactamase-producing Escherichia coli in Thailand

Purpose

Extended-spectrum β-lactamases (ESBLs) have become an issue in community worldwide due to an increase in antibiotic resistance over the past decade. This study was aimed to investigate the phenotypic and genotypic characteristics of ESBL-producing Escherichia coli in Thailand.

Materials and methods

In this study, all clinical isolates collected from tertiary hospitals in Thailand were identified as E. coli by biochemical tests and MALDI-TOF mass spectrometry. ESBL-producing E. coli was preliminary screened with disk diffusion method by cephalosporin disks and confirmed by the method of combination disk diffusion. Antimicrobial susceptibility test was used to determine MIC values of all ESBL-producing E. coli. For genotypic detection, a variety of ESBL genes were determined by PCR. Moreover, multilocus sequence typing (MLST) analysis was performed on internal portions of seven housekeeping genes for the diversity and phylogenetic relatedness of E. coli clonal group.

Results

Of the 285 ESBL-producing E. coli, most were susceptible to carbapenems. These strains showed a high resistance rate to ciprofloxacin (85.26%). The most frequently detected gene was bla_CTX-M1 group at about 71.23% followed by bla_CTX-M9 group (38.95%). The bla_TEM, bla_PER, bla_GES, bla_VEB, and bla_SHV genes were identified in 31.93%, 5.96%, 4.56%, 3.51%, and 0.70% of ESBL-producing isolates, respectively. The bla OXA-10 gene was detected in only one strain. ESBL-producing E. coli isolates with high antimicrobial resistance were further investigated. Among those, E. coli sequence type ST38 was mostly found, followed by ST405, ST410, and ST131. It is noteworthy that the bla_CTX-M gene was mainly detected in all four ST-type E. coli clones (ST38, ST405, ST410, and ST131).

Conclusion

This study provided a recent evidence of the genetic diversity of ESBL-producing E. coli in Thailand. In addition, the profile related to antimicrobial resistance pattern in this region was also demonstrated.

Emerging of a highly pathogenic and multi-drug resistant strain of Escherichia coli causing an outbreak of colibacillosis in chickens

Extraintestinal pathogenic Escherichia coli (ExPEC) are important human pathogens responsible for urinary tract infection and meningitis. Therefore, infection of chickens by highly pathogenic E. coli with multi-drug resistance has become a major concern to food safety. In this study, we isolated a strain of E. coli (HB2016) from the oviduct of a diseased chicken with colibacillosis. Inoculation of chickens with 2 × 10⁶ CFU of the isolate E. coli HB2016 by intraperitoneal injection successfully reproduced colibacillosis in chickens. We also found that E. coli HB2016 harbored four more virulence genes (tsh, trat, cvaC and cvaA/B) than E. coli reference strain CVCC1428. Importantly, E. coli HB2016 was resistant to cefuroxime, tobramycin, medemycin, cefazolin, cefoperazone, streptomycin and ampicillin, and carried multiple antibiotic resistance genes such as strA, strB, bla_CMY-2, bla_CTX-M-19, bla_TEM-1B, fosA, mph(A), floR, sul2, tet(A) and tet(B). These findings suggest that the causative E. coli act as a potential zoonotic agent affecting human health.