ESBL-EC Isolates Research Articles

Increasing Fluroquinolone Susceptibility and Genetic Diversity of ESBL-Producing E. coli from the Lower Respiratory Tract during the COVID-19 Pandemic.

Lower respiratory tract infections (LRTIs) are the fourth leading cause of death worldwide, among which Escherichia coli (E. coli) pneumonia is considered a rare phenomenon. Treatment options for LRTIs have become limited, especially for extended-spectrum β-lactamase-producing E. coli (ESBL-EC), which are usually resistant to other groups of antimicrobials as well. The aim of our study was to compare the phenotypic resistance profiles and genotypes of ESBL-EC isolates associated with LRTIs before (pre-COVID-19) and during (COVID-19) the COVID-19 pandemic. All isolates were screened for antimicrobial resistance genes (ARGs) and virulence-associated genes (VAGs) and assigned to phylogenetic groups, sequence types and clonal groups by PCR. During the pandemic, a significantly lower proportion of ciprofloxacin-, levofloxacin- and trimethoprim-sulfamethoxazole-resistant ESBL-EC isolates was retrieved from lower respiratory tract (LRT) samples. PCR-based genotypization revealed greater clonal diversity and a significantly lower proportion of isolates with blaTEM, aac(6')-Ib-cr and qacEΔ1 genes. In addition, a higher proportion of isolates with the integrase gene int1 and virulence genes sat and tsh was confirmed. The lower prevalence of fluoroquinolone resistance and greater genetic diversity of ESBL-EC isolated during the COVID-19 period may have been due to the introduction of new bacterial strains into the hospital environment, along with changes in clinical establishment guidelines and practices.

Extra-intestinal pathogenic lineages of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are associated with prolonged ESBL gene carriage.

Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) are frequently acquired during international travel, contributing to the global spread of antimicrobial resistance. Human-adapted ESBL-Ec are predicted to exhibit increased intestinal carriage duration, resulting in a higher likelihood of onward human-to-human transmission. Yet, bacterial determinants of increased carriage duration are unknown. Previous studies analysed small traveller cohorts, with short follow-up times, or did not employ high-resolution molecular typing, and were thus unable to identify bacterial traits associated with long-term carriage after recent acquisition. We aimed to identify which ESBL-Ec lineages are associated with increased carriage duration after return from international travel. In a prospective cohort study of 2001 international travellers, we analysed 160 faecal ESBL-Ec isolates from all 38 travellers who acquired ESBL-Ec during travel and subsequently carried ESBL-Ec for at least 12 months after return, by whole-genome sequencing. For 17 travellers, we confirmed the long-term carriage of ESBL-Ec strains through single nucleotide variant typing. To identify determinants of increased carriage duration, we compared the 17 long-term carriers (≥12 months of carriage) with 33 age-, sex- and destination-matched short-term carriers (<1 month of carriage). Long-read sequencing was employed to investigate long-term ESBL plasmid carriage. We show that in healthy travellers with very low antibiotic usage, extra-intestinal pathogenic lineages of E. coli (ExPEC) are significantly more likely to persist than other E. coli lineages. The long-term carriage of E. coli from ExPEC lineages is mainly driven by sequence type 131 and phylogroup D E. coli. Although ExPEC lineages frequently cause extra-intestinal infections such as bloodstream infections, our results indicate that ExPEC lineages are also efficient intestinal colonizers, which potentially contributes to their onward transmission.

Molecular characterization of extended-spectrum β-lactamase-producing Escherichia coli isolated from lower respiratory tract samples between 2002 and 2019 in the Central Slovenia region

BackgroundAntibiotic resistance is one of the most serious global health problems and threatens the effective treatment of bacterial infections. Of greatest concern are infections caused by extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC). The aim of our study was to evaluate the prevalence and molecular characteristics of ESBL-EC isolated over an 18-year pre-COVID period from lower respiratory tract (LRT) samples collected from selected Slovenian hospitals.Objectives and methodsAll isolates were identified by MALDI-TOF and phenotypically confirmed as ESBLs by a disk diffusion assay. Using a PCR approach, 487 non-repetitive isolates were assigned to phylogroups, sequence type groups, and clonal groups. Isolates were also screened for virulence-associated genes (VAGs) and antimicrobial resistance genes.ResultsThe prevalence of ESBL-EC isolates from LRT in a large university hospital was low (1.4%) in 2005 and increased to 10.8% by 2019. The resistance profile of 487 non-repetitive isolates included in the study showed a high frequency of group 1 blaCTX-M (77.4%; n = 377), blaTEM (54.4%; n = 265) and aac(6')-Ib-cr (52%; n = 253) genes and a low proportion of blaSHV and qnr genes. Isolates were predominantly assigned to phylogroup B2 (73.1%; n = 356), which was significantly associated with clonal group ST131. The ST131 group accounted for 67.6% (n = 329) of all isolates and had a higher number of virulence factor genes than the non-ST131 group. The virulence gene profile of ST131 was consistent with that of other extraintestinal pathogenic E. coli (ExPEC) strains and was significantly associated with ten of sixteen virulence factor genes tested. Using ERIC-PCR fingerprinting, isolates with the same ERIC-profile in samples from different patients, and at different locations and sampling dates were confirmed, indicating the presence of “hospital-adapted” strains.ConclusionOur results suggest that the ESBL-EC isolates from LRT do not represent a specific pathotype, but rather resemble other ExPEC isolates, and may be adapted to the hospital environment. To our knowledge, this is the first study of ESBL-EC isolated from LRT samples collected over a long period of time.

Presence of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in Food-Producing and Companion Animals and Wildlife on Small-Holder Farms of Floreana Island, Galápagos Islands.

Background: Antimicrobial resistance (AR) has led to increasing human and animal morbidity and mortality and negative consequences for the environment. AR among Escherichia coli (EC) is on the rise, with serious concerns about extended-spectrum β-lactamase-producing E. coli (ESBL-EC). In the Galápagos Islands, where antimicrobials are available without a prescription, growing demands for food production can drive antimicrobial use. Food producing animals are at the interface of wildlife and environmental health on the smallest human-inhabited Galápagos Island, Floreana. We sought to determine if ESBL-EC were present in Floreana Island farm animal species and nearby wildlife and the relatedness of ESBL-EC isolates identified. Materials and Methods: During July 4-5, 2022, we visited 8 multispecies farms, representing 75% of food-producing animal production on Floreana, and collected 227 fecal samples from farm animals and wildlife. Each sample was plated on MacConkey agar supplemented with cefotaxime (4 μg/mL). Results: ESBL-EC was isolated from 20 (9%) fecal samples collected from pigs (N = 10), chickens (N = 6), wildlife (N = 3), and dog (N = 1). All ESBL-EC isolates were from samples taken at three (38%) of the eight farms. Fifteen (75%) of the ESBL-EC isolates were from a single farm. All ESBL-EC isolates were multidrug resistant. The most prevalent ESBL genes belonged to the blaCTX-M group. Among the typeable isolates from the farm with the largest proportion of ESBL-EC isolates (N = 14), we observed nine unique pulsed-field gel electrophoresis (PFGE) patterns, with identical patterns present across pig and chicken isolates. PFGE patterns in the three farms with ESBL-EC isolates were different. Conclusions: These results lend support for future routine AR monitoring activities at the livestock-wildlife interface in Galápagos to characterize potential interspecies transmission of AR bacteria and AR genes in this unique protected ecosystem, and the related human, animal, and environmental health impacts, and to formulate interventions to reduce AR spread in this setting.

Population structure of community-acquired extended-spectrum beta-lactamase producing Escherichia coli and methicillin resistant Staphylococcus aureus in a French region showed no difference between urban and rural areas.

Antimicrobial resistance is a global health issue and extended-spectrum β-lactamase producing Escherichia coli (ESBL-Ec) and methicillin-resistant Staphylococcus aureus (MRSA) are of particular concern. Whole genome sequencing analysis of isolates from the community is essential to understand the circulation of those multidrug-resistant bacteria. Our main objective was to determine the population structure of clinical ESBL-Ec and MRSA isolated in the community setting of a French region. For this purpose, isolates were collected from 23 sites belonging to 6 private medical biology laboratories in the Bourgogne-Franche-Comté region. One hundred ninety ESBL-Ec and 67 MRSA were sequenced using the Illumina technology. Genomic analyses were performed to determine the bacterial typing, presence of antibiotic resistance genes, metal resistance genes as well as virulence genes. Analysis showed that ST131 was the major ESBL-Ec clone circulating in the region, representing 42.1% of the ESBL-Ec isolates. The blaCTX-M genes represented 98% of blaESBL with the majority being blaCTX-M-15 (53.9%). MRSA population consisted of mainly of CC8 (50.7%) and CC5 (38.8%) clonal complexes. Interestingly, we found a prevalence of 40% of the zinc resistance gene czrC in our MRSA population. We observed no differences in our ESBL-Ec or MRSA populations between urban and rural areas in our French region, suggesting no impact of population density or rural environment.

Presence of blaCTXM-1, blaCTXM-9, and blaTEM-1 Genes in Extended-spectrum β-lactamase-producing Escherichia coli Isolates from Hospital Wastewater

BACKGROUND: Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) are selectively proliferated in the human gut, excreted through feces, and deposited through wastewater lines, with hospital wastewater acting as a major reservoir of antibiotic resistance genes and resistant bacteria, thus pose adverse effects to human health. This study aimed to determine the presence of blaCTXM-1, blaCTXM-9, blaTEM-1, and blaSHV-1 genes in ESBL-EC in wastewater from selected hospitals in Manila and Quezon City, the Philippines.METHODS: Influent and effluent in twelve hospital wastewater treatment plants were collected, screened for cefotaxime-resistant E. coli, and examined for the ESBL production through phenotypic characterization using conventional bacterial identification, disk diffusion method, and VITEK® 2 Compact system and genotypic identification of ESBL-EC blaCTXM-1, blaCTXM-9, blaTEM-1, blaSHV-1 genes using multiplex polymerase chain reaction (PCR).RESULTS: Conventional bacterial identification methods and the VITEK® 2 Compact system results showed that both influent and effluent samples were positive for ESBL-EC at 33.3% and 16.7%, respectively. Multiplex PCR results revealed that various E. coli isolates were of ESBL-EC blaCTXM-1, blaCTXM-9, and blaTEM-1 genes. Multi-drug resistance was observed among all ESBL-EC isolates with resistance being highest against ampicillin, cefuroxime, ceftazidime, ceftriaxone, cefepime, piperacillin, and aztreonam.CONCLUSION: As the study revealed the presence of ESBL-producing bacteria, efforts must be made to ensure the prudent antimicrobial use with possible emphasis on antibiotic rotation accompanied by intensified infection prevention and control in hospital settings.KEYWORDS: antimicrobial resistance, beta-lactams, blaCTXM, blaTEM, extended-spectrum beta-lactamase, E. coli, hospital wastewater

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

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

Prevalence and characterization of ESBL-producing Escherichia coli in healthy pregnant women and hospital environments in Benin: an approach based on Tricycle.

Extended-Spectrum Beta-Lactamase (ESBL)-producing Enterobacterales are recognized as significant pathogens due to their resistance to multiple antibiotics. This study aimed to determine the prevalence of ESBL-producing Escherichia coli (E. coli) in different settings, including healthy pregnant women, the food chain, and the environment of tertiary hospitals in Benin. Samples were collected from various sources, including fecal samples from healthy pregnant women, food samples from hospital canteens, and hospital effluents from four tertiary hospitals in southern Benin. Fecal samples were plated on MacConkey agar supplemented with cefotaxime (4 μg/mL), while food and water samples were plated on Tryptone Bile X agar supplemented with cefotaxime (4 μg/mL). Urea indole tests were used for preliminary identification of E. coli colonies, followed by confirmation of ESBL production using the double disk synergy technique. Antibiotic susceptibility testing of ESBL-producing E. coli strains was conducted using the disk diffusion method on MH agar. Polymerase Chain Reaction (PCR) was used to investigate the presence of ESBL-encoding genes. Among the 296 fecal samples collected from four tertiary hospitals, ESBL-producing E. coli was isolated from 22.30% (66) of the samples. All E. coli isolates from hospital effluents exhibited ESBL production, while ESBL-producing E. coli was not detected in food and drinking water samples. The analysis of variable associations showed no significant associations (p > 0.05) for the studied factors. Antibiotic susceptibility testing revealed high resistance rates among the ESBL-Ec isolates against several tested antibiotics, including amoxicillin, aztreonam, ceftriaxone, ciprofloxacin, and trimethoprim-sulfamethoxazole. However, most isolates remained susceptible to ertapenem, amoxicillin-clavulanate, and imipenem. The most prevalent ESBL-encoding genes were blaTEM (37.50%), blaOXA-1 (19.44%), and blaSHV (11.11%), while a smaller proportion of isolates carried blaCTXM-1/blaCTXM-15 (5.55%) and blaCTXM-9. This study provides insights into the prevalence of ESBL-producing E. coli carriage in the feces of healthy pregnant women in southern Benin. Additionally, it highlights hospital wastewater as a potential reservoir of ESBL-producing bacteria in the environment. The detection of ESBL-producing E. coli in hospital effluents raises concerns about the dissemination of antibiotic resistance genes into the environment. The high resistance rates observed among ESBL-Ec isolates against commonly used antibiotics emphasize the urgent need for antimicrobial stewardship and infection control measures. The identification of prevalent ESBL-encoding genes contributes to understanding the genetic basis of ESBL resistance in the studied population. Further research is warranted to explore the mechanisms of transmission and potential interventions to mitigate the spread of ESBL-producing Enterobacterales.

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.

Community carriage of ESBL-producing Escherichia coli and Klebsiella pneumoniae: a cross-sectional study of risk factors and comparative genomics of carriage and clinical isolates.

The global prevalence of infections caused by extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) is increasing, and for Escherichia coli, observations indicate that this is partly driven by community-onset cases. The ESBL-E population structure in the community is scarcely described, and data on risk factors for carriage are conflicting. Here, we report the prevalence and population structure of fecal ESBL-producing E. coli and Klebsiella pneumoniae (ESBL-Ec/Kp) in a general adult population, examine risk factors, and compare carriage isolates with contemporary clinical isolates. Fecal samples obtained from 4,999 participants (54% women) ≥40 years in the seventh survey of the population-based Tromsø Study, Norway (2015, 2016), were screened for ESBL-Ec/Kp. In addition, we included 118 ESBL-Ec clinical isolates from the Norwegian surveillance program in 2014. All isolates were whole-genome sequenced. Risk factors associated with carriage were analyzed using multivariable logistic regression. ESBL-Ec gastrointestinal carriage prevalence was 3.3% [95% confidence interval (CI) 2.8%-3.9%, no sex difference] and 0.08% (0.02%-0.20%) for ESBL-Kp. For ESBL-Ec, travel to Asia was the only independent risk factor (adjusted odds ratio 3.46, 95% CI 2.18-5.49). E. coli ST131 was most prevalent in both collections. However, the ST131 proportion was significantly lower in carriage (24%) versus clinical isolates (58%, P < 0.001). Carriage isolates were genetically more diverse with a higher proportion of phylogroup A (26%) than clinical isolates (5%, P < 0.001), indicating that ESBL gene acquisition occurs in a variety of E. coli lineages colonizing the gut. STs commonly related to extraintestinal infections were more frequent in clinical isolates also carrying a higher prevalence of antimicrobial resistance, which could indicate clone-associated pathogenicity.IMPORTANCEESBL-Ec and ESBL-Kp are major pathogens in the global burden of antimicrobial resistance. However, there is a gap in knowledge concerning the bacterial population structure of human ESBL-Ec/Kp carriage isolates in the community. We have examined ESBL-Ec/Kp isolates from a population-based study and compared these to contemporary clinical isolates. The large genetic diversity of carriage isolates indicates frequent ESBL gene acquisition, while those causing invasive infections are more clone dependent and associated with a higher prevalence of antibiotic resistance. The knowledge of factors associated with ESBL carriage helps to identify patients at risk to combat the spread of resistant bacteria within the healthcare system. Particularly, previous travel to Asia stands out as a major risk factor for carriage and should be considered in selecting empirical antibiotic treatment in critically ill patients.

Putative transmission of extended-spectrum β-lactamase-producing Escherichia coli among men who have sex with men in Amsterdam, the Netherlands

ObjectivesA previous study showed higher prevalence of Escherichia coli (E. coli) expressing extended-spectrum β-lactamases (ESBL-Ec) among men who have sex with men (MSM) in Amsterdam, the Netherlands, compared with the general Dutch population. This study genetically characterised the ESBL-Ec isolates and investigated whether the increased prevalence could be explained by transmission between participants. MethodsWhole-genome sequences were obtained from 93 unique ESBL-Ec isolates that were cultured from rectal swabs of 79 participants. Isolates were typed according to the Achtman MLST scheme and ESBL and virulence genes were identified. Pairwise SNP distances were determined between isolates. Isolate pairs with ≤ 25 SNPs were considered part of a putative transmission event, and events between multiple participants formed putative transmission clusters. To investigate whether putatively transmitted isolates belonged to globally expanded lineages, the level of hierarchical clustering with international isolates was assessed using core genome MLST (cgMLST) implemented on the Enterobase platform. ResultsThe most frequently detected E. coli types were ST131:blaCTX-M-15 (16 of 117, 13.5%), ST131:blaCTX-M-27, ST3075:blaCTX-M-15 and ST14:blaSHV-12 (all six of 117, 6.5%). Fourteen putative transmission events were identified, forming four putative transmission clusters. The largest putative transmission cluster contained ST131 isolates, which clustered with multiple international isolates in SNP and cgMLST analysis. One other transmission cluster (ST14:blaSHV-12) and two transmission events (ST14:blaSHV-12 and ST394:blaCTX-M-15) contained very rarely reported strains. ConclusionsThe identification of unique ESBL-Ec strains involved in putative transmission and carried by multiple participants demonstrated a high probability of ESBL-Ec transmission between MSM in Amsterdam; therefore, ESBL-Ec infection should be considered in cases of sexually active MSM having associated symptoms.

The risk of pig and chicken farming for carriage and transmission of Escherichia coli containing extended-spectrum beta-lactamase (ESBL) and mobile colistin resistance (mcr) genes in Thailand.

South-East Asian countries report a high prevalence of extended-spectrum cephalosporin- (ESC-) and colistin-resistant Escherichia coli (Col-R-Ec). However, there are still few studies describing the molecular mechanisms and transmission dynamics of ESC-R-Ec and, especially, Col-R-Ec. This study aimed to evaluate the prevalence and transmission dynamics of Ec containing extended spectrum beta-lactamases (ESBL) and mobile colistin resistance (mcr) genes using a 'One Health' design in Thailand. The ESC-R-Ec and Col-R-Ec isolates of human stool samples (69 pig farmers, 155 chicken farmers, and 61 non-farmers), rectal swabs from animals (269 pigs and 318 chickens), and the intestinal contents of 196 rodents were investigated. Resistance mechanisms and transmission dynamics of Ec isolates (n=638) were studied using short and long read sequencing. We found higher rates of ESBL-Ec isolates among pig farmers (n=36; 52.2%) than among chicken farmers (n=58; 37.4 %; P<0.05) and the control group (n=61; 31.1 %; P<0.05). Ec with co-occurring ESBL and mcr genes were found in 17 (6.0 %), 50 (18.6 %) and 15 (4.7 %) samples from humans, pigs and chickens, respectively. We also identified 39 (13.7 %) human samples with non-identical Ec containing ESBL and mcr. We found higher rates of ESBL-Ec, in particular CTX-M-55, isolates among pig farmers than among non-pig farmers (P<0.01). 'Clonal' animal-human transmission of ESBL-Ec and Ec with mcr genes was identified but rare as we overall found a heterogenous population structure of Ec. The Col-R-Ec from human and animal samples often carried mcr-1.1 on conjugative IncX4 plasmids. The latter has been identified in Ec of many different clonal backgrounds.

Effect of a karst system (France) on extended spectrum beta-lactamase (ESBL)-producing Escherichia coli

Karst aquifers are an important water resource worldwide particularly exposed to anthropogenic pollution, including antibiotic-resistance. The release of antibiotic-resistant bacterial pathogens in the environment is a major public health challenge worldwide. In this One Health study, we aimed to determine the effect of karst on antibiotic-resistant bacteria. For this purpose, we determined the concentrations of extended-spectrum β-lactamases-producing Escherichia coli (ESBL-Ec) for 92 weeks in a rural karst hydrosystem providing drinking water. ESBL-Ec isolates (n = 130) were sequenced by whole genome sequencing. We analysed the isolates at different levels of granularity, i.e., phylogroup, sequence type, presence of antibiotic-resistance genes, mutations conferring antibiotic-resistance, and virulence genes. The ESBL-Ec concentrations were spatially and temporally heterogeneous in the studied karst hydrosystem. ESBL-Ec isolates survived in the karst and their concentrations were mostly explained by the hydrodynamic of the hydrosystem. We demonstrate that the studied karst has no filtration effect on ESBL-Ec, either quantitatively (i.e., in the ESBL-Ec concentrations) or qualitatively (i.e., in the genetic characteristics of ESBL-Ec isolates).

ESBL-Producing and Non-ESBL-Producing Escherichia coli Isolates from Urinary Tract Differ in Clonal Distribution, Virulence Gene Content and Phylogenetic Group.

The objectives of this study are to determine the differences in clonality, virulence gene (VG) content and phylogenetic group between non extended-spectrum beta-lactamase-producing E. coli (non-ESBL-EC) and ESBL-EC isolates from urine. This study characterized a total of 100 clinical E. coli isolates consecutively obtained from the inpatients hospitalized in The First Affiliated Hospital of Ningbo University in China by polymerase-chain reaction (PCR). Phylogenetic group B2 was found to be the most prevalent in both ESBL-EC and non-ESBL-EC group. Among 100 clinical isolates, the count of acquired virulence genes in group B2 was found to be significantly higher than that in group A, B1, and D (p <0.001). Additionally, the presence of content within virulence genes (the total number of virulence genes detected per isolate) in B2 of non-ESBL-EC and ESBL-EC showed a significant difference (p<0.001). ST131 was detected exclusively in ESBL-EC, while ST95 and ST73 were the main sequence types in non-ESBL-EC. Our study demonstrated the different distribution of MLST, phylogenetic group in ESBL-EC and non-ESBL-EC group. The inverse association between beta-lactamase resistance and VG content performed in this study should get a lot more attention. At the same time, we should also be wary of the appearance of non-ESBL-EC isolates of group B2 harboring more virulence genes which will lead to high pathogenicity.

Identifying the Sources of Intestinal Colonization With Extended-Spectrum β-Lactamase-Producing Escherichia coli in Healthy Infants in the Community.

The prevalence of fecal colonization with extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) among children in low- and middle-income countries is alarmingly high. This study aimed to identify the sources of ESBL-Ec colonization in children < 1 year old through comparative analysis of E. coli isolates from child stool, child’s mother stool, and point-of-use drinking water from 46 rural households in Bangladesh. The pairwise similarity in antibiotic susceptibility of E. coli from all three sources was evaluated, followed by phylogenetic clustering using enterobacterial repetitive intergenic consensus polymerase chain reaction and whole-genome sequence analysis of the isolates. Matching antibiotic susceptibility and enterobacterial repetitive intergenic consensus polymerase chain reaction patterns were found among ESBL-Ec isolates from child–mother dyads of 24 and 11 households, respectively, from child–water dyads of 5 and 4 households, respectively, and from child–mother–water triads of 3 and 4 households, respectively. Whole-genome sequence analysis of 30 isolates from 10 households revealed that ESBL-Ec from children in five households (50%) was clonally related to ESBL-Ec either from their mothers (2 households), drinking water sources (2 households), or both mother and drinking-water sources (1 household) based on serotype, phylogroup, sequence type, antibiotic resistance genes, mobile genetic elements, core single-nucleotide polymorphisms, and whole-genome multilocus sequence typing. Overall, this study provides empirical evidence that ESBL-Ec colonization in children is linked to the colonization status of mothers and exposure to the household environments contaminated with ESBL-Ec. Interventions such as improved hygiene practices and a safe drinking water supply may help reduce the transmission of ESBL-Ec at the household level.

One Health compartmental analysis of ESBL-producing Escherichia coli on Reunion Island reveals partitioning between humans and livestock.

BackgroundExtended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) is a major cause of infections worldwide. An understanding of the reservoirs and modes of transmission of these pathogens is essential, to tackle their increasing frequency.ObjectivesWe investigated the contributions of various compartments (humans, animals, environment), to human colonization or infection with ESBL-Ec over a 3 year period, on an island.MethodsThe study was performed on Reunion Island (Southwest Indian Ocean). We collected ESBL-Ec isolates prospectively from humans, wastewater and livestock between April 2015 and December 2018. Human specimens were recovered from a regional surveillance system representative of the island’s health facilities. These isolates were compared with those from livestock and urban/rural wastewater, by whole-genome sequencing.ResultsWe collected 410 ESBL-Ec isolates: 161 from humans, 161 from wastewater and 88 from animals. Phylogenomic analysis demonstrated high diversity (100 STs), with different STs predominating among isolates from humans (ST131, ST38, ST10) and animals (ST57, ST156). The large majority (90%) of the STs, including ST131, were principally associated with a single compartment. The CTX-M-15, CTX-M-27 and CTX-M-14 enzymes were most common in humans/human wastewater, whereas CTX-M-1 predominated in animals. Isolates of human and animal origin had different plasmids carrying blaCTX-M genes, with the exception of a conserved IncI1-ST3 blaCTX-M-1 plasmid.ConclusionsThese molecular data suggest that, despite their high level of contamination, animals are not a major source of the ESBL-Ec found in humans living on this densely populated high-income island. Public health policies should therefore focus primarily on human-to-human transmission, to prevent human infections with ESBL-Ec.

A Descriptive Analysis of Urinary ESBL-Producing-Escherichia coli in Cerdanya Hospital.

Urinary tract infections caused by extended-spectrum β-lactamase Escherichia coli (ESBL-EC) are increasing worldwide and are a current concern because treatment options are often limited. This study investigated antimicrobial susceptibility, antimicrobial resistance genes (ARGs), and the biological diversity of urinary ESBL-EC isolates at Cerdanya Hospital, a European cross-border hospital that combines French and Spanish healthcare models. Bacterial identification and susceptibility were determined using the Microscan WalkAway® system and ESBL production was examined by the double-disk synergy method. Isolates were sequenced using the Ion S5™ next-generation sequencing system, with the whole-genome sequences then assembled using SPADEs software and analyzed using PubMLST, ResFinder, FimTyper, PlasmidFinder, and VirulenceFinder. A phylogenetic analysis was performed by constructing an assembly-based core-SNV alignment, followed by a phylogenetic tree constructed using Parsnp from the Harvest suite. All isolates studied were multidrug-resistant and could be classified into 19 different sequence types characterized by a high genetic diversity. The most prevalent ESBL-enzymes were CTX-M-14 and CTX-M-15. High-risk international clones (ST131, ST10, and ST405) were also identified. The results demonstrated the absence of a single predominant clone of ESBL-MDR-EC at Cerdanya Hospital.

Prevalence and Molecular Epidemiology of Extended-Spectrum-β-Lactamase (ESBL)-Producing Escherichia coli from Multiple Sectors of Poultry Industry in Korea.

The aim of this study was to investigate the molecular epidemiology of extended-spectrum-β-lactamase producing Escherichia coli (ESBL-EC) from poultry, the poultry farm environment, and workers in Korea. A total of 1376 non-duplicate samples were collected from 21 poultry farms, 20 retail stores, 6 slaughterhouses, and 111 workers in a nationwide study in Korea from January 2019 to August 2019. The overall positive rate of ESBL-EC was 6.8%, with variable positive rates according to sources (0.9% of worker, 5.2% of poultry, 10.0% of chicken meat, and 14.3% of environment). Common ESBL types were CTX-M-55 and CTX-M-14 in a total of 93 ESBL-EC isolates. Whole genome sequencing revealed that 84 ESBL-EC isolates had an outstanding accumulation of numerous antimicrobial resistance (AMR) genes associated with resistance to various classes of antimicrobials for human use and well-known antimicrobial gene (ARG)-carrying plasmids. Core gene multi locus sequence typing, using 2390 core genes, indicated no dominant clone or common type in each province. In conclusion, the isolation rates of ESBL-EC were not negligible in the poultry industry-related samples, sharing common ESBL types of human ESBL-EC isolates in Korea.

Antibiotic Resistance Pattern of Extended Spectrum Beta Lactamase Producing Escherichia coli Isolated From Patients With Urinary Tract Infection in Morocco.

Extended-spectrum β-lactamases producing Escherichia coli (ESBL-EC) lend resistance to most β-lactam antibiotics. Because of limited treatment options, ESBL-EC infections are generally more difficult to treat, leading to higher hospital costs, reduced rates of microbiological and clinical responses, and a threat to the patient’s life. This study aimed to determine the antibiotic resistance pattern of ESBL-EC isolated from patients with urinary tract infection in Morocco. This retrospective laboratory-based study was conducted at Cheikh Khalifa International University Hospital, Casablanca, from January 2016 to June 2019. A total of 670 urine samples were collected from urinary tract infection patients and processed by standard microbiological methods. In vitro susceptibility testing to different antibiotics of all identified isolates of Escherichia coli (E. coli) was performed following Kirby–Bauer’s disc diffusion method on Mueller–Hinton Agar according to the EUCAST standards. The reviewing of ESBL-EC was confirmed by the appearance of a characteristically shaped zone referred to as a “champagne cork” using the Combined Disk Test. Among a total of 438 E. coli isolated from nonrepetitive urine samples, two hundred fifty-nine (59%) were ESBL-EC, of which 200 (77%) were isolated from adult patients (over the age of 50) and the majority were female. All ESBL-EC isolates were resistant to third-generation cephalosporin and quinolones and sensitive to carbapenem and fosfomycin. Knowledge of antimicrobial resistance patterns in ESBL-EC, the major pathogen associated with urinary tract infection, is indispensable as a guide in choosing empirical antimicrobial treatment.

Prevalence and Molecular Epidemiology of Extended-Spectrum-β-Lactamase (ESBL)-Producing Escherichia coli From Multiple Sectors of the Swine Industry in Korea: A Korean Nationwide Monitoring Program for a One Health Approach to Combat Antimicrobial Resistance.

BackgroundOne health is a flexible concept with many facets, including the environment, community, and the nosocomial super-bacteria resistance network. We investigated the molecular prevalence of extended-spectrum-β-lactamase-producing Escherichia coli (ESBL-EC) in workers, livestock, and the farm environment in Korea.MethodsESBL-EC isolates were obtained from samples from 19 swine farms, 35 retail stores, seven slaughterhouses, and 45 related workers throughout Korea from August 2017 to July 2018, using ChromID ESBL (BioM?rieux, Marcy l’Etoile, France) agar and enrichment broth. The presence of ESBL and mobilized colistin resistance (mcr) genes and antimicrobial resistance were determined. Clonality was evaluated with pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).ResultsIn total, 232 ESBL-EC isolates were obtained from 1,614 non-duplicated samples (14.4% positive rate). The ESBL-EC isolates showed regional and source-related differences. blaCTX-M-55 (N=100), blaCTX-M-14 (N=65), blaCTX-M-15 (N=33), and blaCTX-M-65 (N=23) were common ESBL types. The ESBL-EC isolates showed high resistance rates for various antimicrobial classes; however, all isolates were susceptible to carbapenem. One swine-originating colistin-resistant isolate did not carry any known mcr gene. PFGE was successful for 197 of the 232 isolates, and most PFGE types were heterogeneous, except for some dominant PFGE types (O, R, T, U, and V). MLST of 88 isolates was performed for representative PFGE types; however, no dominant sequence type was observed.ConclusionsThe proportion of ESBL-EC in swine industry-related samples was significant, and the isolates harbored common clinical ESBL gene types. These molecular epidemiologic data could provide important evidence for antimicrobial-resistance control through a one health approach.