A review of the mechanisms that confer antibiotic resistance in pathotypes of E. coli

The dissemination of antibiotic resistance in Escherichia coli poses a significant threat to public health worldwide. This review provides a comprehensive update on the diverse mechanisms employed by E. coli in developing resistance to antibiotics. We primarily focus on pathotypes of E. coli (e.g., uropathogenic E. coli) and investigate the genetic determinants and molecular pathways that confer resistance, shedding light on both well-characterized and recently discovered mechanisms. The most prevalent mechanism continues to be the acquisition of resistance genes through horizontal gene transfer, facilitated by mobile genetic elements such as plasmids and transposons. We discuss the role of extended-spectrum β-lactamases (ESBLs) and carbapenemases in conferring resistance to β-lactam antibiotics, which remain vital in clinical practice. The review covers the key resistant mechanisms, including: 1) Efflux pumps and porin mutations that mediate resistance to a broad spectrum of antibiotics, including fluoroquinolones and aminoglycosides; 2) adaptive strategies employed by E. coli, including biofilm formation, persister cell formation, and the activation of stress response systems, to withstand antibiotic pressure; and 3) the role of regulatory systems in coordinating resistance mechanisms, providing insights into potential targets for therapeutic interventions. Understanding the intricate network of antibiotic resistance mechanisms in E. coli is crucial for the development of effective strategies to combat this growing public health crisis. By clarifying these mechanisms, we aim to pave the way for the design of innovative therapeutic approaches and the implementation of prudent antibiotic stewardship practices to preserve the efficacy of current antibiotics and ensure a sustainable future for healthcare.

Prevalence and characterization of antimicrobial-resistant Escherichia coli in chicken meat from wet markets in Hong Kong

Given the close contact between animals, animal products, and consumers in wet markets, fresh meat products are considered a potential source and disseminator of antimicrobial-resistant (AMR) bacteria near the end of the food chain. This cross-sectional study was conducted to estimate the prevalence of select AMR-E. coli in fresh chicken meat collected from wet markets in Hong Kong and to determine target genes associated with the observed resistance phenotypes. Following a stratified random sampling design, 180 fresh half-chickens were purchased from 29 wet markets across Hong Kong in 2022 and immediately processed. After incubation, selective isolation was performed for extended-spectrum β-lactamase producing (ESBL), carbapenem-resistant (CRE), and colistin-resistant (CSR) E. coli. The bacterial isolates were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Disc Diffusion was used to determine the susceptibility of ESBL- and CRE-E. coli isolates. The broth microdilution method was used to determine the minimum inhibitory concentration of CSR-E. coli. Targeted resistance genes were then detected by PCR. The prevalence of ESBL-E. coli and CSR-E. coli were estimated at 88.8% (95% CI: 83.4-93.1%) and 6.7% (95% CI: 3.5-11.4%), respectively. No CRE-E. coli isolate was detected. The blaCTX-M-1 gene was the most common β-lactamase group in isolated E. coli (80%), followed by blaTEM (63.7%); no blaSHV gene was detected. Forty-five percent of the isolates had blaTEM and blaCTX-M-1 simultaneously. The mcr-1 gene was detected in all 12 CSR isolates. Of 180 meat samples, 59 were from Mainland China, and 121 were locally sourced. There was no statistically significant difference in the prevalence of ESBL- and CSR-E. coli between the two sources. Our findings can be used to inform food safety risk assessments and set the stage for adopting targeted control and mitigation measures tailored to the local wet markets.

Extended-spectrum β-lactamases producing Enterobacteriaceae (ESBL-PE) prevalence in Nepal: A systematic review and meta-analysis

An alarming increase in the occurrence of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) has threatened the treatment and management of bacterial infections. This systematic review and meta-analysis aimed to provide a quantitative estimate of the prevalence of ESBL among the members of the Enterobacteriaceae family by analyzing the community-based and clinical studies published between 2011 and 2021 from Nepal and determine if ESBL-PE correlates with multidrug resistance (MDR). The Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines were followed for systematic review and meta-analysis and the articles' quality was assessed using the Newcastle-Ottawa scale. Of the 2529 articles screened, 65 articles were systematically reviewed, data extracted, and included in in-depth meta-analysis. The overall pooled prevalence of ESBL-producers in Enterobacteriaceae was 29 % (95 % CI: 26-32 %) with high heterogeneity (I2 = 96 %, p < 0.001). Escherichia coli was the predominant ESBL-producing member of the Enterobacteriaceae family, followed by Citrobacter spp. and Klebsiella spp. The prevalence of ESBL-PE increased from 18.7 % in 2011 to 29.5 % in 2021. A strong positive correlation (r = 0.98) was observed between ESBL production and MDR in Enterobacteriaceae. ESBL-PE isolates showed high resistance to ampicillin, cephalosporins, and amoxicillin-clavulanic acid, and blaCTX-M type was the most reported gene variant among ESBL-PE. In conclusion, this study demonstrated an increased prevalence of ESBL-PE in Nepal over the last decade, and such isolates showed a high level of MDR against the β-lactams and non-β-lactam antibiotics. Tackling the rising antibiotic resistance (AR) and MDR in ESBL-PE would require concerted efforts from all stakeholders to institute effective infection control programs in the community and clinical settings.

Drug-microbiota interactions: an emerging priority for precision medicine

Individual variability in drug response (IVDR) can be a major cause of adverse drug reactions (ADRs) and prolonged therapy, resulting in a substantial health and economic burden. Despite extensive research in pharmacogenomics regarding the impact of individual genetic background on pharmacokinetics (PK) and pharmacodynamics (PD), genetic diversity explains only a limited proportion of IVDR. The role of gut microbiota, also known as the second genome, and its metabolites in modulating therapeutic outcomes in human diseases have been highlighted by recent studies. Consequently, the burgeoning field of pharmacomicrobiomics aims to explore the correlation between microbiota variation and IVDR or ADRs. This review presents an up-to-date overview of the intricate interactions between gut microbiota and classical therapeutic agents for human systemic diseases, including cancer, cardiovascular diseases (CVDs), endocrine diseases, and others. We summarise how microbiota, directly and indirectly, modify the absorption, distribution, metabolism, and excretion (ADME) of drugs. Conversely, drugs can also modulate the composition and function of gut microbiota, leading to changes in microbial metabolism and immune response. We also discuss the practical challenges, strategies, and opportunities in this field, emphasizing the critical need to develop an innovative approach to multi-omics, integrate various data types, including human and microbiota genomic data, as well as translate lab data into clinical practice. To sum up, pharmacomicrobiomics represents a promising avenue to address IVDR and improve patient outcomes, and further research in this field is imperative to unlock its full potential for precision medicine.

Antibiotic resistance and virulence genes profiling of Vibrio cholerae and Vibrio mimicus isolates from some seafood collected at the aquatic environment and wet markets in Eastern Cape Province, South Africa

The current study determines the density of Vibrio spp. and isolates V. cholerae and Vibrio mimicus from fish-anatomical-sites, prawn, crab and mussel samples recovered from fish markets, freshwater and brackish water. Virulence and antibiotic resistance profiling of isolates were carried out using standard molecular and microbiology techniques. Vibrio spp. was detected in more than 90% of samples [134/144] and its density was significantly more in fish than in other samples. Vibrio. cholerae and V. mimicus were isolated in at least one sample of each sample type with higher isolation frequency in fish samples. All the V. cholerae isolates belong to non-O1/non-O139 serogroup. One or more V. cholerae isolates exhibited intermediate or resistance against each of the eighteen panels of antibiotics used but 100% of the V. mimicus were susceptible to amikacin, gentamycin and chloramphenicol. Vibrio cholerae exhibited relatively high resistance against polymyxin, ampicillin and amoxicillin/clavulanate while V. mimicus isolates exhibited relatively high resistance against nitrofurantoin, ampicillin and polymixin. The multiple-antibiotic-resistance-index [MARI] for isolates ranges between 0 and 0.67 and 48% of the isolates have MARI that is >0.2 while 55% of the isolates exhibit MultiDrug Resistance Phenotypes. The percentage detection of acc, ant, drf18, sul1, mcr-1, blasvh, blaoxa, blatem, blaoxa48, gyrA, gyrB and parC resistance-associated genes were 2%, 9%, 14%, 7%, 2%, 25%, 7%, 2%, 2%, 32%, 25% and 27% respectively while that for virulence-associated genes in increasing other was ace [2%], tcp [11%], vpi [16%], ompU [34%], toxR [43%], rtxC [70%], rtxA [73%] and hyla [77%]. The study confirmed the potential of environmental non-O1/non-O139 V. cholerae and V. mimicus to cause cholera-like infection and other vibriosis which could be difficult to manage with commonly recommended antibiotics. Thus, regular monitoring of the environment to create necessary awareness for this kind of pathogens is important in the interest of public health.

Effect of Group Housing of Preweaned Dairy Calves: Health and Fecal Commensal Antimicrobial Resistance Outcomes

The objectives of this study were to investigate the effects of group housing (three calves per group) on bovine respiratory disease (BRD), diarrhea and antimicrobial resistance (AMR) to fecal commensal Escherichia coli (EC) and enterococci/streptococci (ES). Our study comprised two arms, one experimental and one observational. In the experimental arm, preweaned calves on a California dairy were randomized to either individual (IND; n = 21) or group (GRP; n = 21) housing, using a modified California-style wooden hutch. The study period lasted from birth to 56 days of age, during which calves were health scored daily. Cumulative incidence and hazard ratios were estimated for disease. Antimicrobial resistance outcomes were assessed using a prospective cohort design; feces were collected from each calf three times per week and EC and ES were evaluated for AMR using the broth microdilution method against a panel of 19 antimicrobial drugs (AMD). Analysis of treatment records was used to select calves that had been exposed (EXP) to an AMD-treated calf. In GRP, exposure occurred when a calf was a hutchmate with an AMD-treated calf. In IND, exposure occurred when a calf was a neighbor with an AMD-treated calf (TRT). Age-matched unexposed calves (UNEXP) were then selected for comparison. Proportions of AMR in fecal commensals among EXP, UNEXP, and TRT calves were compared between GRP and IND. Accelerated failure time survival regression models were specified to compare differences in minimum inhibitory concentration (MIC) of fecal commensals between EXP and UNEXP calves within each of GRP and IND calves separately. Group calves had a BRD hazard 1.94 times greater that of IND calves (p = 0.03), using BRD treatment records as the outcome. For AMR in EC isolates, higher resistance to enrofloxacin was detected in enrofloxacin-EXP GRP isolates compared with enrofloxacin-EXP IND isolates, and UNEXP GRP calves had lower resistance to ceftiofur compared with enrofloxacin-EXP and enrofloxacin-TRT calves. A significant housing-by-time interaction was detected for EC ceftiofur MIC in EXP GRP calves at 4-14 days post exposure to enrofloxacin (MIC EXP-UNEXP: µg/mL (95% CI): 10.62 (1.17, 20.07)), compared with UNEXP calves. The findings of this study show an increase in BRD hazard for group-housed calves and an increase in ceftiofur resistance in group-housed calves exposed to an enrofloxacin-treated calf.

Antimicrobial Resistance in Romania: Updates on Gram-Negative ESCAPE Pathogens in the Clinical, Veterinary, and Aquatic Sectors

Multidrug-resistant Gram-negative bacteria such as Acinetobacter baumannii, Pseudomonas aeruginosa, and members of the Enterobacterales order are a challenging multi-sectorial and global threat, being listed by the WHO in the priority list of pathogens requiring the urgent discovery and development of therapeutic strategies. We present here an overview of the antibiotic resistance profiles and epidemiology of Gram-negative pathogens listed in the ESCAPE group circulating in Romania. The review starts with a discussion of the mechanisms and clinical significance of Gram-negative bacteria, the most frequent genetic determinants of resistance, and then summarizes and discusses the epidemiological studies reported for A. baumannii, P. aeruginosa, and Enterobacterales-resistant strains circulating in Romania, both in hospital and veterinary settings and mirrored in the aquatic environment. The Romanian landscape of Gram-negative pathogens included in the ESCAPE list reveals that all significant, clinically relevant, globally spread antibiotic resistance genes and carrying platforms are well established in different geographical areas of Romania and have already been disseminated beyond clinical settings.

Antibiotic Resistance among Gastrointestinal Bacteria in Broilers: A Review Focused on Enterococcus spp. and Escherichia coli

Chickens can acquire bacteria at different stages, and bacterial diversity can occur due to production practices, diet, and environment. The changes in consumer trends have led to increased animal production, and chicken meat is one of the most consumed meats. To ensure high levels of production, antimicrobials have been used in livestock for therapeutic purposes, disease prevention, and growth promotion, contributing to the development of antimicrobial resistance across the resident microbiota. Enterococcus spp. and Escherichia coli are normal inhabitants of the gastrointestinal microbiota of chickens that can develop strains capable of causing a wide range of diseases, i.e., opportunistic pathogens. Enterococcus spp. isolated from broilers have shown resistance to at least seven classes of antibiotics, while E. coli have shown resistance to at least four. Furthermore, some clonal lineages, such as ST16, ST194, and ST195 in Enterococcus spp. and ST117 in E. coli, have been identified in humans and animals. These data suggest that consuming contaminated animal-source food, direct contact with animals, or environmental exposure can lead to the transmission of antimicrobial-resistant bacteria. Therefore, this review focused on Enterococcus spp. and E. coli from the broiler industry to better understand how antibiotic-resistant strains have emerged, which antibiotic-resistant genes are most common, what clonal lineages are shared between broilers and humans, and their impact through a One Health perspective.

β-Lactamase Producing Escherichia coli Encoding blaCTX-M and blaCMY Genes in Chicken Carcasses from Egypt

Escherichia coli with multidrug resistance and β-lactamase genes may constitute a great public health hazard due to the potential for their transmission to humans through the food chain. This study determined the prevalence, antibiotic resistance profiles, phylogroups, and β-lactamase genes of E. coli isolates from chicken carcasses marketed in Mansoura, Egypt. Interestingly, E. coli was detected in 98% (98/100) of the chicken carcasses examined, which seemed among the highest contamination rates by E. coli worldwide. From the 425 genetically verified uidA gene-positive E. coli, 85 isolates were further studied for antimicrobial resistance profiles, phylogroups, and β-lactamase genes. Interestingly, 89.41% of E. coli (76/85) strains tested against 24 different antibiotics were multidrug-resistant. Of the examined 85 E. coli isolates, 22 (25.88%) isolates harbored bla_CTX-M and were resistant to ampicillin, cefazoline, and ceftriaxone, while three of them were resistant to ceftazidime besides. Nine (10.59%) E. coli strains harbored AmpC- β-lactamase bla_CMY and were resistant to ampicillin. One isolate co-carried bla_CMY and bla_CTX-M genes, though it was negative for the bla_TEM gene. Of the 35 isolates that harbored either extended-spectrum β-lactamase (ESBL) and/or AmpC β-lactamase genes, six strains (17.14%) were assigned to pathogenic phylogroup F and one to phylogroup E, whereas 28 (80%) isolates belonged to commensal phylogenetic groups.

Zoo animal manure as an overlooked reservoir of antibiotic resistance genes and multidrug-resistant bacteria

Animal fecal samples collected in the summer and winter from 11 herbivorous animals, including sable antelope (SA), long-tailed goral (LTG), and common eland (CE), at a public zoo were examined for the presence of antibiotic resistance genes (ARGs). Seven antibiotics, including meropenem and azithromycin, were used to isolate culturable multidrug-resistant (MDR) strains. The manures from three animals (SA, LTG, and CE) contained 10⁴-fold higher culturable MDR bacteria, including Chryseobacterium, Sphingobacterium, and Stenotrophomonas species, while fewer MDR bacteria were isolated from manure from water buffalo, rhinoceros, and elephant against all tested antibiotics. Three MDR bacteria-rich samples along with composite samples were further analyzed using nanopore-based technology. ARGs including lnu(C), tet(Q), and mef(A) were common and often associated with transposons in all tested samples, suggesting that transposons carrying ARGs may play an important role for the dissemination of ARGs in our tested animals. Although several copies of ARGs such as aph(3')-IIc, bla_L1, bla_IND-3, and tet(42) were found in the sequenced genomes of the nine MDR bacteria, the numbers and types of ARGs appeared to be less than expected in zoo animal manure, suggesting that MDR bacteria in the gut of the tested animals had intrinsic resistant phenotypes in the absence of ARGs.

Examining the impact of zinc on horizontal gene transfer in Enterobacterales

Antimicrobial resistance is one of the main international health concerns for humans, animals, and the environment, and substantial efforts have focused on reducing its development and spread. While there is evidence for correlations between antimicrobial usage and antimicrobial resistance development, specific information on the effect of heavy metal/antimicrobial usage on bacterial conjugation is more limited. The aim of this study was to investigate the effects of zinc and antimicrobials in different concentrations on horizontal gene transfer of an ampicillin resistance gene, using a multi-drug resistant Escherichia coli donor strain and three different Salmonella enterica serovars as recipient strains. Differences in conjugation frequencies for the different Salmonella recipients were observed, independent of the presence of zinc or the antimicrobials. Selective pressure on the recipient strains, in the form of ampicillin, resulted in a decrease in conjugation frequencies, while, the presence of rifampicin resulted in increases. Zinc exposure affected conjugation frequencies of only one of the three recipient strains, thus the effect of zinc on conjugation frequencies seemed to be concentration and strain dependent. Furthermore, differences in growth rates due to plasmid carriage were observed for one of the Salmonella strains.

Zoonotic Risks of Sleeping with Pets

Background: Pets are increasingly becoming part of the family and interactions between pets and their owners is changing. This results in extended and more intimate contact between owners and their pets, which give rise to zoonotic risks. Objective: To establish the presence of potential zoonotic pathogens in pets that sleep with their owner. Methods: As a pilot study, a group of 28 healthy dogs and 22 healthy cats were monitored for the presence of the zoonotic parasites Cheyletiella, Ctenocephalides spp. and Toxocara spp., the dermatophyte Microsporum canis, and the bacteria Clostridium difficile, Salmonella spp., Campylobacter jejuni and Enterobacteriaceae. This was investigated by taking samples from the fur, the footpads and the animal bed. The owners filled in a questionnaire. Results: In total, 29 of the 50 pets (58%) slept on the bed, of which 15 pets (30%) slept in the bed (under the blankets). A total of 19/22 dogs (86%) and 7/22 cats (32%) tested positive for Enterobacteriaceae on the fur or footpads. Fleas were found in 5/22 of the cats’ (23%) and 2/28 of the dogs’ (7%) favourite sleeping spots. High levels of aerobic colonies were found, up to 216 colony forming units/cm². Other pathogens were not found in this study. Conclusions: The results of this preliminary study confirm literature reports that pets may constitute a potential risk in the transmission of zoonotic pathogens to their owner, especially during direct contact when sleeping in the same bed. Owners should therefore be informed about these risks and educated to interact with their pets in a more responsible way.

Distribution and Genomic Characterization of Third-Generation Cephalosporin-Resistant Escherichia coli Isolated from A Single Family and Home Environment: A 2-Year Longitudinal Study

Third-generation cephalosporin-resistant Escherichia coli (CREC), particularly strains producing extended-spectrum β-lactamases (ESBLs), are a global concern. Our study aims to longitudinally assemble the genomic characteristics of CREC isolates from fecal samples from an index patient with recurrent CREC-related urinary tract infections and his family and swabs from his home environment 12 times between 2019 and 2021 to investigate the distribution of antibiotic resistance genes. CREC identified using the VITEK 2 were subjected to nanopore whole-genome sequencing (WGS). The WGS of 27 CREC isolates discovered in 137 specimens (1 urine, 123 feces, and 13 environmental) revealed the predominance of ST101 and ST131. Among these sequence types, bla_CTX-M (44.4%, n = 12) was the predominant ESBL gene family, with bla_CTX-M-14 (n = 6) being the most common. The remaining 15 (55.6%) isolates harbored bla_CMY-2 genes and were clonally diverse. All E. coli isolated from the index patient’s initial urine and fecal samples belonged to O25b:H4-B2-ST131 and carried bla_CTX-M-14. The results of sequence analysis indicate plasmid-mediated household transmission of bla_CMY-2 or bla_CTX-M-55. A strong genomic similarity was discovered between fecal ESBL-producing E. coli and uropathogenic strains. Furthermore, bla_CMY-2 genes were widely distributed among the CREC isolated from family members and their home environment.

Antibiotic resistance genes of public health importance in livestock and humans in an informal urban community in Nepal

Efforts to mitigate the increasing emergence of antimicrobial resistance (AMR) will benefit from a One Health perspective, as over half of animal antimicrobials are also considered medically important in humans, and AMR can be maintained in the environment. This is especially pertinent to low- and middle-income countries and in community settings, where an estimated 80% of all antibiotics are used. This study features AMR genes found among humans, animals, and water at an urban informal settlement in Nepal with intensifying livestock production. We sampled humans, chickens, ducks, swine, and water clustered by household, as well as rodents and shrews near dwellings, concurrently in time in July 2017 in southeastern Kathmandu along the Manohara river. Real-time qualitative PCR was performed to screen for 88 genes. Our results characterize the animal-human-environmental interfaces related to the occurrence of specific resistance genes (bla_SHV-1 (SHV(238G240E) strain), QnrS, ermC, tetA, tetB, aacC2, aadA1) associated with antibiotics of global health importance that comprise several drug classes, including aminoglycosides, beta-lactams, tetracyclines, macrolides, and fluoroquinolones. By characterizing risk factors across AMR genes of public health importance, this research highlights potential transmission pathways for further investigation and provides prioritization of community-based prevention and intervention efforts for disrupting AMR transmission of critically important antibiotics used in both humans and animals in Nepal.

Cross-Sectional Survey of Antibiotic Resistance in Extended Spectrum β-Lactamase-Producing Enterobacteriaceae Isolated from Pigs in Greece

Simple Summary

The objective of this study was to investigate, for the first time in Greece, the prevalence of ESBL producers in swine populations and to correlate their occurrence with risk factors. A total of 214 fecal samples were collected from the farms from December 2019 to April 2021. A subset of 78 (78/214, 36.5%) ESBL producers were identified as Escherichia coli (E. coli, 88.5%), Klebsiella pneumoniae spp. pneumoniae (K. pneumoniae, 3.8%), Proteus mirabilis (P. mirabilis, 5.1%), Enterobacter cloacae complex (E. cloacae complex, 1.3%) and Salmonella enterica spp. diarizonae (S. enterica spp. diarizonae, 1.3%). CTX-M, SHV and TEM genes were detected along with genes conferring resistance to fluoroquinolones, aminoglycosides, sulfonamides, trimethoprim, macrolides and colistin. This study displayed high antimicrobial resistance rates in the Greek swine industry, and our results are alarming for both human and animal health.

Abstract

This study aimed to estimate the prevalence of extended-spectrum β-lactamase-producing (ESBL) bacteria in swine. Thus, 214 fecal samples were collected from suckling and weaned piglets from 34 farms in Greece (out of an overall population of about 14,300 sows). A subset of 78 (36.5%) ESBL producers were identified as E. coli (69/78, 88.5%), K. pneumoniae spp. pneumoniae (3.8%), P. mirabilis (5.1%), E. cloacae complex (1.3%) and S. enterica spp. diarizonae (1.3%). Resistance to at least one class of non-β-lactam antibiotics was detected in 78 isolates. Among the E. coli strains, resistance was identified with regard to aminoglycosides (n = 31), fluoroquinolones (n = 49), tetracycline (n = 26) and trimethoprim/sulfamethoxazole (n = 46). Of the three K. pneumoniae spp. pneumoniae, two displayed resistances to aminoglycosides and all were resistant to fluoroquinolones, tetracyclines and trimethoprim/sulfamethoxazole. As for the four P. mirabilis isolates, three had a resistant phenotype for aminoglycosides and all were resistant to imipenem, fluoroquinolones, tetracyclines and trimethoprim/sulfamethoxazole. Molecular characterization of the isolates revealed the presence of CTX-M, SHV and TEM genes, as well as of genes conferring resistance to fluoroquinolones, aminoglycosides, sulfonamides, trimethoprim, macrolides and colistin. High levels of antimicrobial resistance (AMR) were demonstrated in Greek swine herds posing a concern for the efficacy of treatments at the farm level as well as for public health.

Prevalence of extended-spectrum β-lactamase-producing Enterobacterales in retail sheep meat from Zagazig city, Egypt

Background

The goal of this study was to investigate the prevalence of extended-spectrum β-lactamase production in Enterobacterales isolated from retail sheep meat in Zagazig, Egypt.

Methods

One hundred random samples of sheep meat were collected from different retail butcher shops (n = 5) in the city of Zagazig, Egypt. Bacterial isolates were identified by MALDI-TOF MS and screened for antibiotic susceptibility by disk diffusion; further genotypic characterization of β-lactamase-encoding genes was performed with Real-Time PCR. E. coli strains were phylotyped with the Clermont triplex PCR method.

Results

Of the total of 101 bacterial isolates recovered from retail sheep meat samples, 93 were E. coli, six were Enterobacter cloacae and two were Proteus mirabilis. As many as 17% of these 100 samples showed ESBL phenotypes, all were E. coli. The bla_CTX-M genes were detected in seven isolates (six were bla_CTX-M-15 and one was bla_CTX-M-14), three isolates harboured bla_TEM (all were bla_TEM-one), and two carried genes of the bla_SHV family (both were bla_SHV-12). Eight E. coli isolates expressed ESBL phenotype but no bla_TEM, bla_SHV or bla_CTX-M genes were detected by PCR. ESBL- positive E. coli isolates were nearly equally distributed over the commensal groups A/B1 and the virulent group D.

Conclusion

Nearly one in five sheep meat samples was contaminated with ESBL-E. coli. This further corroborates the potential role played by contaminated meat in the increasing resistance rates that have been reported worldwide.

Wildlife and Antibiotic Resistance

Antibiotic resistance is a major human health problem. While health care facilities are main contributors to the emergence, evolution and spread of antibiotic resistance, other ecosystems are involved in such dissemination. Wastewater, farm animals and pets have been considered important contributors to the development of antibiotic resistance. Herein, we review the impact of wildlife in such problem. Current evidence supports that the presence of antibiotic resistance genes and/or antibiotic resistant bacteria in wild animals is a sign of anthropic pollution more than of selection of resistance. However, once antibiotic resistance is present in the wild, wildlife can contribute to its transmission across different ecosystems. Further, the finding that antibiotic resistance genes, currently causing problems at hospitals, might spread through horizontal gene transfer among the bacteria present in the microbiomes of ubiquitous animals as cockroaches, fleas or rats, supports the possibility that these organisms might be bioreactors for the horizontal transfer of antibiotic resistance genes among human pathogens. The contribution of wildlife in the spread of antibiotic resistance among different hosts and ecosystems occurs at two levels. Firstly, in the case of non-migrating animals, the transfer will take place locally; a One Health problem. Paradigmatic examples are the above mentioned animals that cohabit with humans and can be reservoirs and vehicles for antibiotic resistance dissemination. Secondly, migrating animals, such as gulls, fishes or turtles may participate in the dissemination of antibiotic resistance across different geographic areas, even between different continents, which constitutes a Global Health issue.

GENOMIC CHARACTERIZATION OF MULTIDRUG-RESISTANT EXTENDED-SPECTRUM β-LACTAMASE-PRODUCING ESCHERICHIA COLI AND KLEBSIELLA PNEUMONIAE FROM CHIMPANZEES (PAN TROGLODYTES) FROM WILD AND SANCTUARY LOCATIONS IN UGANDA

Farm and wild animals may serve as reservoirs of antimicrobial-resistant bacteria of human health relevance. We investigated the occurrence and genomic characteristics of extended spectrum β-lactamase (ESBL)-producing bacteria in Ugandan chimpanzees (Pan troglodytes) residing in two environments with or without close contact to humans. The ESBL-producing Escherichia coli and Klebsiella pneumoniae were isolated from fecal material of chimpanzees from Budongo Forest and Ngamba Island Chimpanzee Sanctuary in Uganda and were more commonly isolated from chimpanzees in Ngamba Island Chimpanzee Sanctuary, where animals have close contact with humans. Selected ESBL isolates (E. coli n=9, K. pneumoniae n=7) were analyzed by whole-genome sequencing to determine the presence of resistance genes, as well as sequence type and virulence potential; the blaCTX-M-15 gene was present in all strains. Additionally, the ESBL genes blaSHV-11 and blaSHV-12 were found in strains in the study. All strains were found to be multidrug resistant. The E. coli strains belonged to four sequence types (ST2852, ST215, ST405, and ST315) and the K. pneumoniae strains to two sequence types (ST1540 and ST597). Virulence genes did not indicate that strains were of common E. coli pathotype, but strains with the same sequence types as isolated in the current study have previously been reported from clinical cases in Africa. The findings indicate that chimpanzees in close contact with humans may carry ESBL bacteria at higher frequency than those in the wild, indicating a potential anthropogenic transmission.

A Farm-to-Fork Quantitative Microbial Exposure Assessment of β-Lactam-Resistant Escherichia coli among U.S. Beef Consumers

Integrated quantitative descriptions of the transmission of β-lactam-resistant Escherichia coli (BR-EC) from commercial beef products to consumers are not available. Here, a quantitative microbial exposure assessment model was established to simulate the fate of BR-EC in a farm-to-fork continuum and provide an estimate of BR-EC exposure among beef consumers in the U.S. The model compared the per-serving exposures from the consumption of intact beef cuts, non-intact beef cuts, and ground beef. Additionally, scenario analysis was performed to evaluate the relative contribution of antibiotic use during beef cattle production to the level of human exposure to BR-EC. The model predicted mean numbers of BR-EC of 1.7 × 10⁻⁴, 8.7 × 10⁻⁴, and 6.9 × 10⁻¹ CFU/serving for intact beef cuts, non-intact beef cuts, and ground beef, respectively, at the time of consumption. Sensitivity analyses using the baseline model suggested that factors related to sectors along the supply chain, i.e., feedlots, processing plants, retailers, and consumers, were all important for controlling human exposure to BR-EC. Interventions at the processing and post-processing stages are expected to be most effective. Simulation results showed that a decrease in antibiotic use among beef cattle might be associated with a reduction in exposure to BR-EC from beef consumption. However, the absolute reduction was moderate, indicating that the effectiveness of restricting antibiotic use as a standalone strategy for mitigating human exposure to BR-EC through beef consumption is still uncertain. Good cooking and hygiene practices at home and advanced safety management practices in the beef processing and post-processing continuum are more powerful approaches for reducing human exposure to antibiotic-resistant bacteria in beef products.

Clinical Perspective of Antimicrobial Resistance in Bacteria

Antimicrobial resistance (AMR) has become a global clinical problem in recent years. With the discovery of antibiotics, infections were not a deadly problem for clinicians as they used to be. However, worldwide AMR comes with the overuse/misuse of antibiotics and the spread of resistance is deteriorated by a multitude of mobile genetic elements and relevant resistant genes. This review provides an overview of the current situation, mechanism, epidemiology, detection methods and clinical treatment for antimicrobial resistant genes in clinical important bacteria including methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE), penicillin-resistant Streptococcus pneumoniae (PRSP), extended-spectrum β-lactamase-producing Enterobacteriaceae, acquired AmpC β-lactamase-producing Enterobacteriaceae, carbapenemase-producing Enterobacteriaceae (CPE), multidrug-resistant (MDR) Acinetobacter baumannii and Pseudomonas aeruginosa.

Beta-lactamase resistance genes in Enterobacteriaceae from Nigeria

Background

Beta-lactamase genes are one of the most important groups of antimicrobial resistance genes in human and animal health. Therefore, continuous surveillance of this group of resistance genes is needed for a better understanding of the local epidemiology within a country and global dissemination.

Aim

This review was carried out to identify different beta-lactamase resistance genes reported in published literature from Nigeria.

Methods

Systematic review and meta-analysis was carried out on eligible Nigerian articles retrieved from electronic literature searches of PubMed^®, African Journals Online, and Google Scholar published between January 1990 and December 2019. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses method was adopted to facilitate clarity and transparency in reporting review findings.

Results

Fifty-seven articles were included. All beta-lactamases reported were detected from Gram-negative bacteria, particularly from Enterobacteriaceae. Thirty-six different beta-lactamase genes were reported in Nigeria. These genes belong to the narrow-spectrum, AmpC, extended-spectrum and carbapenemase beta-lactamase resistance genes. The pooled proportion estimate of extended-spectrum beta-lactamase genes in Nigeria was 31% (95% confidence interval [CI]: 26% – 36%, p < 0.0001), while the estimate of the bla_CTX-M-15 gene in Nigeria was 46% (95% CI: 36% – 57%, p < 0.0001). The proportion estimate of AmpC genes was 32% (95% CI: 11% – 52%, p < 0.001), while the estimate for carbapenemases was 8% (95% CI: 5% – 12%, p < 0.001).

Conclusion

This study provides information on beta-lactamase distribution in Nigeria. This is necessary for a better understanding of molecular epidemiology of clinically important beta-lactamases, especially the extended-spectrum beta-lactamases and carbapenemases in Nigeria.

Presence of the Extended-Spectrum-β-Lactamase and Plasmid-Mediated AmpC-Encoding Genes in Escherichia coli from Companion Animals-A Study from a University-Based Veterinary Hospital in Taipei, Taiwan

Extended-spectrum-β-lactamase (ESBL) and AmpC β-lactamase are two enzymes commonly found in Enterobacteriaceae that confer resistance to major antibiotics, such as third-generation cephalosporins that are widely prescribed for both human and animals. We screened for Escherichia coli producing ESBL and plasmid-mediated AmpC β-lactamase (pAmpC) from dogs and cats brought to National Taiwan University Veterinary Hospital, Taipei, Taiwan from 29 June 2020, to 31 December 2020. The genotypes and phylogenetic relatedness of these E. coli were also analyzed. Fifty samples of E. coli obtained from 249 bacterial isolates were included in this study. Among them, eight isolates had ESBL, seven had pAmpC, and one had both. Thirty-two percent (16/50) of E. coli isolates were resistant to third-generation cephalosporins. The detected ESBL genes included the bla_CTX-M-1 and bla_CTX-M-9 groups, and the bla_CMY-2 group was the only gene type found in pAmpC. ESBL-producing E. coli belonged to the pathogenic phylogroup B2, and the sequence types (STs) were ST131 and ST1193. Three isolates were determined to be ST131-O25b, a highly virulent epidemic clone. The pAmpC-producing E. coli were distributed in multiple phylogroups, primarily the commensal phylogroup B1. The STs of the pAmpC-producing E. coli included ST155, ST315, ST617, ST457, ST767, ST372, and ST93; all of these have been reported in humans and animals. Imipenem was active against all the ESBL/pAmpC-producing E. coli; however, since in humans it is a last-resort antimicrobial, its use in companion animals should be restricted.

Detection of virulence and extended spectrum β-lactamase genes in Salmonella by multiplex high-resolution melt curve real-time PCR assay

AIMS

Develop and standardize multiplex high-resolution melt curve (HRM) real-time PCR assays for simultaneous detection of Salmonella virulence and extended spectrum β-lactamase (ESBL) genes in food.

METHODS AND RESULTS

Two sets of multiplex real-time PCR assays targeting six virulence and three ESBL genes with internal amplification control were standardized. The first assay detected hilA, fimH, sipA, bla_TEM and bla_SHV, and the second detected invA, fimA, stn and bla_CMY . The PCR assays were validated with DNA samples from 77 different Salmonella strains. The assay specificity was tested with DNA from 47 non-Salmonella strains. Melt curve analyses showed distinct, well-separated melting peaks of each target gene detected by their respective melting temperatures (T_m ). Different food samples were spiked with 10, 10² and 10³  CFU/ml of Salmonella. The optimized assays were able to detect all target genes in concentrations of as low as 10 CFU/ml in 25 g foods within 10 h of enrichment.

CONCLUSIONS

Multiplex HRM real-time PCR assays can be used as rapid detection methods for detecting Salmonella in foods.

SIGNIFICANCE AND IMPACT OF STUDY

The assays developed in this study will allow for accurate detection of virulence and ESBL genes in Salmonella that are present in low concentrations in food samples.

Genetic Background of Antimicrobial Resistance in Multiantimicrobial-Resistant Escherichia coli Isolates from Feces of Healthy Broiler Chickens in Tunisia

Multiantimicrobial-resistant Escherichia coli isolates are a global human health problem causing increasing morbidity and mortality. Genes encoding antimicrobial resistance are mainly harbored on mobile genetic elements (MGEs) such as transposons and plasmids as well as integrons, which enhance their rapid spread. The aim of this study was to characterize 83 multiantimicrobial-resistant E. coli isolates recovered from healthy broiler chickens. Among 78 tetracycline-resistant isolates, the tetA, tetB, and tetC genes were detected in 59 (75.6%), 14 (17.9%), and one (1.2%) isolates, respectively. The sul1, sul2, and sul3 genes were detected 31 (46.2%), 16 (23.8%), and 6 (8.9%) isolates, respectively, among 67 sulfonamide-resistant isolates. The PCR-based replicon typing method showed plasmids in 29 isolates, IncFIB (19), IncI1-Iγ (17), IncF (14), IncK (14), IncFIC (10), IncP (8), IncY (3), IncHI2 (1), and IncX (1). The class 1 and 2 integrons were detected in 57 and 2 isolates, respectively; one isolate harbored both integrons. Seven and one gene cassette arrays were identified in class 1 and class 2 integrons, respectively. Our findings show that multiantimicrobial-resistant E. coli isolates from chickens serve as reservoirs of highly diverse and abundant tet and sul genes and plasmid replicons. Such isolates and MGEs pose a potential health threat to the public and animal farming.

Global colistin use: A review of the emergence of resistant Enterobacterales and the impact on their genetic basis

The dramatic global rise of MDR and XDR Enterobacterales in human medicine forced clinicians to the reintroduction of colistin as last-resort drug. Meanwhile, colistin is used in the veterinary medicine since its discovery, leading to a steadily increasing prevalence of resistant isolates in the livestock and meat-based food sector. Consequently, transmission of resistant isolates from animals to humans, acquisition via food and exposure to colistin in the clinic are reasons for the increased prevalence of colistin-resistant Enterobacterales in humans in the last decades. Initially, resistance mechanisms were caused by mutations in chromosomal genes. However, since the discovery in 2015, the focus has shifted exclusively to mobile colistin resistances (mcr). This review will advance the understanding of chromosomal-mediated resistance mechanisms in Enterobacterales. We provide an overview about genes involved in colistin resistance and the current global situation of colistin-resistant Enterobacterales. A comparison of the global colistin use in veterinary and human medicine highlights the effort to reduce colistin sales in veterinary medicine under the One Health approach. In contrast, it uncovers the alarming rise in colistin consumption in human medicine due to the emergence of MDR Enterobacterales, which might be an important driver for the increasing emergence of chromosome-mediated colistin resistance.

Screening of Epidemiologically Significant Mechanisms of Antibiotics to β-Lactams in Enterobacteriaceae - Pathogens of Zoonoses

Among the acquired mechanisms of resistance to antibiotics of microorganisms, the production of beta-lactamases, enzymes that inactivate penicillins, cephalosporins, carbapenems, and monobactams, is widespread. Most often, such beta-lactamases, in particular ESBL (extended-spectrum beta-lactamases), are capable of destroying III and IV generations of cephalosporins. One of the important ESBL producers is Escherichia coli and, to a lesser extent, Salmonella enteritidis, which are clinically significant in animals and humans. The purpose of the study was to screen ESBL DDM using cephalosporin markers and screening of mobile extrachromosomal factors of bacterial heredity – plasmids (potentially dangerous factors of genetic transport) in isolates of E. coli and S. enteritidis, polyresistant to aminoderms, from environmental objects, patho- and biological material, raw materials and products of animal origin. Results of our studies have shown the level of their distribution among animals, poultry, since from 13 field isolates of E. coli isolated from the milk of cows with mastitis and pathological material from pigs, ESBL production was found in 3 strains (23.1%) and from 18 field isolates of S. enteritidis isolated from pathological material from poultry, ESBL production was found in 2 strains (11.1%). Based on the results of molecular genetics studies, the presence of resistance plasmids (R-plasmids) in 9 field E. coli isolates was confirmed, 4 of which produced acquired beta-lactamases, incl. ESBL and 8 field isolates of S. enteritidis, 7 of which confirmed the presence of acquired carbapenemases.

Inactivation, removal, and regrowth potential of opportunistic pathogens and antimicrobial resistance genes in recycled water systems

With two thirds of the global population living in areas affected by water scarcity, wastewater reuse is actively being implemented or explored by many nations. There is a need to better understand the efficacy of recycled water treatment plants (RWTPs) for removal of human opportunistic pathogens and antimicrobial resistant microorganisms. Here, we used a suite of probe-based multiplex and SYBR green real-time PCR assays to monitor enteric opportunistic pathogens (EOPs; Acinetobacter baumannii, Arcobacter butzlieri, Escherichia coli, Enterococcus faecalis, Klebsiella pneumoniae, Legionella spp., Listeria monocytogenes, Pseudomonas aeruginosa, Salmonella Enteritidis, Streptococcus spp.) and antimicrobial resistance genes (ARGs; qnrS, bla_SHV, bla_TEM, bla_GES, bla_KPC, bla_IMI, bla_SME, bla_NDM, bla_VIM, bla_IMP, bla_OXA-48-like, mcr-1 and mcr-3) of key concern from an antimicrobial resistance (AMR), waterborne and foodborne disease perspective. The class 1 integron-integrase gene (intl1) was quantified as a proxy for multi-drug resistance. EOPs, intl1 and ARGs absolute abundance (DNA and RNA) and metabolic activity (RNA) was assessed through three RWTPs with differing treatment trains. Our results indicate that RWTPs produced high quality recycled water for non-potable reuse by removing >95% of EOPs and ARGs, however, subpopulations of EOPs and ARGs survived disinfection and demonstrated potential to become actively growing members of the recycled water and distribution system microbiomes. The persistence of functional intl1 suggests that significant genetic recombination capacity remains in the recycled water, along with the likely presence of multi-drug resistant bacteria. Results provide new insights into the persistence and growth of EOPs, and prevalence and removal of ARGs in recycled water systems. These data will contribute towards the emerging evidence base of AMR risks in recycled water to inform quantitative risk-based policy development regarding water recycling schemes.

Comparison of Antimicrobial-Resistant Escherichia coli Isolates from Urban Raccoons and Domestic Dogs

Wildlife can be exposed to antimicrobial-resistant bacteria (ARB) via multiple pathways. Spatial overlap with domestic animals is a prominent exposure pathway. However, most studies of wildlife-domestic animal interfaces have focused on livestock and little is known about the wildlife-companion animal interface. Here, we investigated the prevalence and phylogenetic relatedness of extended-spectrum cephalosporin-resistant (ESC-R) Escherichia coli from raccoons (Procyon lotor) and domestic dogs (Canis lupus familiaris) in the metropolitan area of Chicago, IL, USA. To assess the potential importance of spatial overlap with dogs, we explored whether raccoons sampled at public parks (i.e., parks where people and dogs could enter) differed in prevalence and phylogenetic relatedness of ESC-R E. coli to raccoons sampled at private parks (i.e., parks where people and dogs could not enter). Raccoons had a significantly higher prevalence of ESC-R E. coli (56.9%) than dogs (16.5%). However, the richness of ESC-R E. coli did not vary by host species. Further, core single-nucleotide polymorphism (SNP)-based phylogenetic analyses revealed that isolates did not cluster by host species, and in some cases displayed a high degree of similarity (i.e., differed by less than 20 core SNPs). Spatial overlap analyses revealed that ESC-R E. coli were more likely to be isolated from raccoons at public parks than raccoons at private parks, but only for parks located in suburban areas of Chicago, not urban areas. That said, ESC-R E. coli isolated from raccoons did not genetically cluster by park of origin. Our findings suggest that domestic dogs and urban/suburban raccoons can have a diverse range of ARB, some of which display a high degree of genetic relatedness (i.e., differ by less than 20 core SNPs). Given the differences in prevalence, domestic dogs are unlikely to be an important source of exposure for mesocarnivores in urbanized areas. IMPORTANCE Antimicrobial-resistant bacteria (ARB) have been detected in numerous wildlife species across the globe, which may have important implications for human and animal health. Wildlife can be exposed to ARB via numerous pathways, including via spatial overlap with domestic animals. However, the interface with domestic animals has mostly been explored for livestock and little is known about the interface between wild animals and companion animals. Our work suggests that urban and suburban wildlife can have similar ARB to local domestic dogs, but local dogs are unlikely to be a direct source of exposure for urban-adapted wildlife. This finding is important because it underscores the need to incorporate wildlife into antimicrobial resistance surveillance efforts, and to investigate whether certain urban wildlife species could act as additional epidemiological pathways of exposure for companion animals, and indirectly for humans.

Molecular characterization of ESBL- producing uropathogenic Escherichia coli recovered from urine samples of patients attending a University Teaching hospital in Nigeria

Infection of the urinary tract ranks as one of the most common infections affecting people worldwide and its treatment is made complicated by the rising incidence of antibiotic resistance. This study aimed to detect extended spectrum beta-lactamase (ESBL) genes and antibiotic resistance profile of uropathogenic Escherichia coli (E. coli) recovered from patients attending a University Teaching hospital in Nigeria. Uropathogenic E. coli isolates were obtained from the culture collection of Department of Microbiology and Parasitology of the University Teaching hospital for a period of four months (October 2019-January, 2020). Antibiotic susceptibility testing was done using the disc diffusion method while phenotypic ESBL production was detected using double disc synergy test (DDST). Detection of β-lactamase genes was done using Real-Time PCR. Forty-nine E. coli isolates were recovered from 120 urine samples, with 24 (49%) being ESBL positive. The resistance to antibiotics in the ESBL producers was: ciprofloxacin (100%), cefotaxime (100%), cefpodoxime (100%), tetracycline (95.7%), ceftazidime (56.7%), amoxicillin-clavulanate (50%), gentamicin (33.3%), and imipenem (0%). All the ESBL producers carried blaTEM, blaCTX-M-1 and blaCTX-M-9, 75% (18/24) carried blaSHV, while blaCTX-M-2, blaCTX-M-8 and blaCTX-M-25 groups were detected in 20.8% (5/24) of the isolates. There was co-occurrence of CTX-M, SHV and TEM β-lactamases in 79.2% (19/24) isolates, while five isolates (20.8%) co-harbored blaCTX-M and blaTEM. This study showed a high level of multidrug resistance and ESBL gene carriage in uropathogenic E. coli obtained in this study, suggesting a likely review of therapeutic options in the treatment of UTI to clamp down on the rising cases of antibiotic resistance.

Resistance Detection and Transmission Risk Analysis of Pig-Derived Pathogenic Escherichia coli in East China

Objective: Antibiotics play an essential role in the treatment and prevention of diseases in pig farms. However, the irrational use of antibiotics leads to the emergence of multi-drug resistance of bacteria, which poses a critical threat to the efficacy of antibiotic treatments. Therefore, the study is designed to analyze the drug resistance of pathogenic Escherichia coli isolated from large-scale pig farms in East China, which provides a theoretical basis for precisely targeted clinical drugs in swine farms. Method: The pathogenic E. coli were isolated and identified from clinical samples of swine farms, and the drug resistance of pathogenic E. coli was detected by antimicrobial susceptibility test (AST) and minimum inhibitory concentration test (MIC). Moreover, the prevalence of plasmid-mediated β-lactam resistance genes was analyzed by PCR. Results: A total of 67 pathogenic E. coli were isolated from 152 samples collected from 20 large-scale pig farms in East China. All isolated pathogenic E. coli are associated with severe drug resistance. Moreover, 70% of isolated pathogenic E. coli is resistant to more than four antibiotics. Besides, there were 19 serotypes including O2, O4, O5, O6, O14, O26, O38, O42, O49, O57, O92, O93, O95, O101, O121, O131, O143, O158, and O161, of which the O4 and O92 serotype were the main serotypes in swine farms. The main extended-spectrum beta-lactamases (ESBLs)-encoding genes in East China were bla _CTX-M, bla _TEM, and bla _OXA by the detection of the ESBLs encoding genes of porcine pathogenic E. coli. The conjugation assays showed that a total of 30 transconjugants were obtained by conjugation, which indicated that drug resistance genes could be transmitted horizontally through conjugative plasmids. Conclusion: The isolated pathogenic E. coli were all multi-drug resistant, and especially O4 and O92 were the main serotypes. The β-lactam resistance genes were prevalent in large-scale pig farms in East China, which provided a theoretical basis for the prevention and control of pig-derived pathogenic E. coli in the future.

ESBL-Producing Escherichia coli Carrying CTX-M Genes Circulating among Livestock, Dogs, and Wild Mammals in Small-Scale Farms of Central Chile

Antibiotic-resistant bacteria of critical importance for global health such as extended-spectrum beta-lactamases-producing (ESBL)-Escherichia coli have been detected in livestock, dogs, and wildlife worldwide. However, the dynamics of ESBL-E. coli between these animals remains poorly understood, particularly in small-scale farms of low and middle-income countries where contact between species can be frequent. We compared the prevalence of fecal carriage of ESBL-E. coli among 332 livestock (207 cows, 15 pigs, 60 horses, 40 sheep, 6 goats, 4 chickens), 82 dogs, and wildlife including 131 European rabbits, 30 rodents, and 12 Andean foxes sharing territory in peri-urban localities of central Chile. The prevalence was lower in livestock (3.0%) and wildlife (0.5%) compared to dogs (24%). Among 47 ESBL-E. coli isolates recovered, CTX-M-group 1 was the main ESBL genotype identified, followed by CTX-M-groups 2, 9, 8, and 25. ERIC-PCR showed no cluster of E. coli clones by either host species nor locality. To our knowledge, this is the first report of ESBL-E. coli among sheep, cattle, dogs, and rodents of Chile, confirming their fecal carriage among domestic and wild animals in small-scale farms. The high prevalence of ESBL-E. coli in dogs encourages further investigation on their role as potential reservoirs of this bacteria in agricultural settings.

Presence of Broad-Spectrum Beta-Lactamase-Producing Enterobacteriaceae in Zoo Mammals

Broad-spectrum beta-lactamase (BSBL)-producing Enterobacteriaceae impose public health threats. With increased popularity of zoos, exotic animals are brought in close proximity of humans, making them important BSBL reservoirs. However, not much is known on the presence of BSBLs in zoos in Western Europe. Fecal carriage of BSBL-producing Enterobacteriaceae was investigated in 38 zoo mammals from two Belgian zoos. Presence of bla-genes was investigated using PCR, followed by whole-genome sequencing and Fourier-transform infrared spectroscopy to cluster acquired resistance encoding genes and clonality of BSBL-producing isolates. Thirty-five putatively ceftiofur-resistant isolates were obtained from 52.6% of the zoo mammals. Most isolates were identified as E. coli (25/35), of which 64.0% showed multidrug resistance (MDR). Most frequently detected bla-genes were CTX-M-1 (17/25) and TEM-1 (4/25). Phylogenetic trees confirmed clustering of almost all E. coli isolates obtained from the same animal species. Clustering of five isolates from an Amur tiger, an Amur leopard, and a spectacled bear was observed in Zoo 1, as well as for five isolates from a spotted hyena and an African lion in Zoo 2. This might indicate clonal expansion of an E. coli strain in both zoos. In conclusion, MDR BSBL-producing bacteria were shown to be present in the fecal microbiota of zoo mammals in two zoos in Belgium. Further research is necessary to investigate if these bacteria pose zoonotic and health risks.

Detection of bla OXA-1, bla TEM-1, and Virulence Factors in E. coli Isolated From Seals

Marine mammals are frequently considered good sentinels for human, animal and environmental health due to their long lifespan, coastal habitat, and characteristics as top chain predators. Using a One Health approach, marine mammals can provide information that helps to enhance the understanding of the health of the marine and coastal environment. Antimicrobial resistance (AMR) is the quintessential One Health problem that poses a well-recognised threat to human, animal, and ecosystem health worldwide. Treated and untreated sewage, hospital waste and agricultural run-off are often responsible for the spread of AMR in marine and freshwater ecosystems. Rescued seals (n = 25) were used as sentinels to investigate the levels of AMR in the Irish coastal ecosystem. Faecal swabs were collected from these animals and bacterial isolates (E. coli and cefotaxime-resistant non-E. coli) from each swab were selected for further investigation. E. coli isolates were characterised in terms of phylogenetic group typing, AMR, and virulence factors. All E. coli isolates investigated in this study (n = 39) were ampicillin resistant while 26 (66.6%) were multi-drug resistant (MDR). Resistance genes bla _OXA-1 and bla _TEM-1 were detected in 16/39 and 6/39 isolates, respectively. Additionally, virulence factors associated with adhesion (sfa, papA, and papC) and siderophores (fyuA and iutA) were identified. An additional 19 faecal cefotaxime-resistant non-E. coli isolates were investigated for the presence of β-lactamase encoding genes. These isolates were identified as presumptive Leclercia, Pantoea and Enterobacter, however, none were positive for the presence of the genes investigated. To the authors knowledge this is the first study reporting the detection of bla _OXA-1 and bla _TEM-1 in phocid faecal E. coli in Europe. These results highlight the importance of marine mammals as sentinels for the presence and spread of AMR in the marine and coastal environment.

Low airborne tenacity and spread of ESBL-/AmpC-producing Escherichia coli from fertilized soil by wind erosion

ESBL-/AmpC-producing Escherichia coli from organic fertilizers were previously detected on soil surfaces of arable land and might be emitted by wind erosion. To investigate this potential environmental transmission path, we exposed ESBL-/AmpC-positive chicken litter, incorporated in agricultural soils, to different wind velocities in a wind tunnel and took air samples for microbiological analysis. No data exist concerning the airborne tenacity of ESBL-/AmpC-producing E. coli. Therefore, we explored the tenacity of two ESBL/AmpC E. coli strains and E. coli K12 in aerosol chamber experiments at different environmental conditions. In the wind tunnel, ESBL/AmpC-producing E. coli were detected in none of the air samples (n = 66). Non-resistant E. coli were qualitatively detected in 40.7% of air samples taken at wind velocities exceeding 7.3 m s^-1 . Significantly increased emission of total viable bacteria with increasing wind velocity was observed. In the aerosol chamber trials, recovery rates of airborne E. coli ranged from 0.003% to 2.8%, indicating a low airborne tenacity. Concluding, an emission of ESBL/AmpC E. coli by wind erosion in relevant concentrations appears unlikely because of the low concentration in chicken litter compared with non-resistant E. coli and their low airborne tenacity, proven in the aerosol chamber trials.

Multidrug Resistance Dissemination in Escherichia coli Isolated from Wild Animals: Bacterial Clones and Plasmid Complicity

Objectives. Epidemiological data concerning third-generation cephalosporin (3GC) resistance in wild fauna are scarce. The aim of this study was to characterize the resistance genes, their genetic context, and clonal relatedness in 17 Escherichia coli resistant to 3GC isolated from wild animals. Methods. The isolates were characterized by short-read whole genome sequencing, and long-read sequencing was used for the hybrid assembly of plasmid sequences. Results. The 3GC resistance gene most identified in the isolates was the extended-spectrum β-lactamases (ESBL)-encoding gene blaCTX-M-1 (82.3%), followed by blaCTX-M-32 (5.9%), blaCTX-M-14 (5.9%), and blaSHV-12 (5.9%). E. coli isolates mainly belonged to the sequence types (STs) rarely reported from humans. The single nucleotide polymorphism (SNP)-based typing showed that most E. coli genomes from wild animals (wild boars, birds of prey, and buzzards) formed clonal clusters (<5 SNPs), showing a clonal dissemination crossing species boundaries. blaCTX-M-1-harboring IncI1-ST3 plasmid was the predominant ESBL-encoding plasmid (76.4%) in wild animal isolates. Plasmid comparison revealed a 110-kb self-transferable plasmid consisting of a conserved backbone and two variable regions involved in antimicrobial resistance and in interaction with recipient cells during conjugation. Conclusion. Our results highlighted the unexpected clonal dissemination of blaCTX-M-1-encoding clones and the complicity of IncI1-ST3 plasmid in the spread of blaCTX-M-1 within wild fauna.

Detection of ESBL/AmpC-Producing and Fosfomycin-Resistant Escherichia coli From Different Sources in Poultry Production in Southern Brazil

This study discussed the use of antimicrobials in the commercial chicken production system and the possible factors influencing the presence of Extended-spectrum β-lactamase (ESBL)/AmpC producers strains in the broiler production chain. The aim of this study was to perform longitudinal monitoring of ESBL-producing and fosfomycin-resistant Escherichia coli from poultry farms in southern Brazil (Paraná and Rio Grande do Sul states) and determine the possible critical points that may be reservoirs for these strains. Samples of poultry litter, cloacal swabs, poultry feed, water, and beetles (Alphitobius sp.) were collected during three distinct samplings. Phenotypic and genotypic tests were performed for characterization of antimicrobial resistant strains. A total of 117 strains were isolated and 78 (66%) were positive for ESBL production. The poultry litter presented ESBL positive strains in all three sampled periods, whereas the cloacal swab presented positive strains only from the second period. The poultry litter represents a significant risk factor mainly at the beginning poultry production (odds ratio 6.43, 95% confidence interval 1-41.21, p < 0.05). All beetles presented ESBL positive strains. The predominant gene was bla CTX-M group 2, which occurred in approximately 55% of the ESBL-producing E. coli. The cit gene was found in approximately 13% of the ESBL-producing E. coli as AmpC type determinants. A total of 19 out of 26 fosfomycin-resistant strains showed the fosA3 gene, all of which produced ESBL. The correlation between fosA3 and bla CTX-M group 1 (bla CTX-M55 ) genes was significant among ESBL-producing E. coli isolated from Paraná (OR 3.66, 95% CI 1.9-9.68) and these genetic determinants can be transmitted by conjugation to broiler chicken microbiota strains. Our data revealed that poultry litter and beetles were critical points during poultry production and the presence of fosfomycin-resistant strains indicate the possibility of risks associated with the use of this antimicrobial during production. Furthermore, the genetic determinants encoding CTX-M and fosA3 enzymes can be transferred to E. coli strains from broiler chicken microbiota, thereby creating a risk to public health.

Escherichia coli as Commensal and Pathogenic Bacteria Among Food-Producing Animals: Health Implications of Extended Spectrum β-lactamase (ESBL) Production

Simple Summary

This revision is about the problem of Escherichia coli as a commensal and pathogenic bacterium among food-producing animals and health implications. Escherichia coli may play an important ecological role and can be used as a bioindicator of antimicrobial resistance. All animal species used for food production, as well as humans, carry E. coli in their intestinal tract; plus, the genetic flexibility and adaptability of this bacteria to constantly changing environments allows it to acquire a great number of antimicrobial resistance mechanisms. The majority of E. coli strains are commensals inhabiting the intestinal tract of humans and warm-blooded animals and rarely causes diseases. However, E. coli also remains as one of the most frequent causes of several common bacterial infections in humans and animals. All over the word, antibiotic resistance is commonly detected among commensal bacteria from food-producing animals, raising important questions on the potential impact of antibiotic use in animals and the possible transmission of these resistant bacteria to humans through the food chain. The use, in food-producing animals, of antibiotics that are critically important in human medicine has been implicated in the emergence of new forms of resistant bacteria, including new strains of multidrug-resistant foodborne bacteria, such as extended spectrum β-lactamase (ESBL)-producing E. coli.

Abstract

Escherichia coli are facultative, anaerobic Gram-negative rods with many facets. Within resistant bacterial populations, they play an important ecological role and can be used as a bioindicator of antimicrobial resistance. All animal species used for food production, as well as humans, carry E. coli in their intestinal tracts; plus, the genetic flexibility and adaptability of this bacteria to constantly changing environments allows it to acquire a great number of antimicrobial resistance mechanisms. Thus, the prevalence of antimicrobial resistance in these commensal bacteria (or others, such as enterococci) can be a good indicator for the selective pressure caused by the use of antimicrobial agents, providing an early warning of the emergence of antimicrobial resistance in pathogens. As many as 90% of E. coli strains are commensals inhabiting the intestinal tracts of humans and warm-blooded animals. As a commensal, it lives in a mutually beneficial association with its hosts and rarely causes diseases. However, E. coli also remains as one of the most frequent causes of several common bacterial infections in humans and animals. In humans, it is the prominent cause of enteritis, community- and hospital-acquired urinary tract infection (UTI), septicemia, postsurgical peritonitis, and other clinical infections, such as neonatal meningitis, while, in farm animals, it is more prominently associated with diarrhea. On a global scale, E. coli can be considered the most important human pathogen, causing severe infection along with other major bacterial foodborne agents, such as Salmonella spp. and Campylobacter. Thus, the importance of resistance in E. coli, typically considered a benign commensal, should not be underestimated.

Occurrence of extended-spectrum β-lactamase and AmpC-producing Escherichia coli in retail meat products from the Maritime Provinces, Canada

This study was conducted to determine the occurrence of antimicrobial resistance to the extended-spectrum cephalosporins (ESC) in Escherichia coli isolates. The isolates were collected from retail meat products collected in the Maritime Provinces of Canada. Our analyses involved the use of both selective and traditional culture methods; we also conducted genotype analyses using multiplex polymerase chain reactions. ESC-resistant (ESC-R) E. coli were detected in 33 of 559 samples (5.9%) using the traditional culture method, compared with 151 of 557 samples (27.1%) using the selective culture method. We recovered more isolates of ESC-R E. coli from poultry compared with beef and pork (P < 0.001). Multidrug resistance, extended-spectrum β-lactamase (ESBL), and AmpC phenotypes were more common in chicken-derived isolates than other retail meat products (P < 0.001). From the 98 isolates examined, 76 isolates (77.6%) were positive for either ESBL and AmpC β-lactamases or both. Among the 76 isolates, bla_CMY-2 (78.9%), bla_CTXM (46.1%), bla_TEM (21.1%), and bla_SHV (1.3%) genes were detected. Among the bla_CTXM-producing isolates, bla_CTXM-1, bla_CTXM-2, and bla_CTXM-9 phylogenetic groups were detected. β-lactamase genes were more commonly detected in chicken-derived isolates compared with other meat types (P < 0.01). This study demonstrates the occurrence of ESBL- and AmpC-resistance genes in retail meat products in the Maritime Provinces of Canada. We found that selective culture significantly improved the recovery of ESC-R E. coli isolates from retail meat samples.

Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms

BACKGROUND

The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment. Here, we evaluate the resistome footprint of an extensive pig farming system, maintained for decades, as compared to that of industrialized intensive pig farming by analyzing 105 fecal, environmental and slurry metagenomes from 38 farms.

RESULTS

Our results evidence a significantly higher abundance of antimicrobial resistance genes (ARGs) on intensive farms and a link between AMU and AMR to certain antimicrobial classes. We observed differences in the resistome across sample types, with a higher richness and dispersion of ARGs within environmental samples than on those from feces or slurry. Indeed, a deeper analysis revealed that differences among the three sample types were defined by taxa-ARGs associations. Interestingly, mobilome analyses revealed that the observed AMR differences between intensive and extensive farms could be linked to differences in the abundance of mobile genetic elements (MGEs). Thus, while there were no differences in the abundance of chromosomal-associated ARGs between intensive and extensive herds, a significantly higher abundance of integrons in the environment and plasmids, regardless of the sample type, was detected on intensive farms.

CONCLUSIONS

Overall, this study shows how AMU, production system, and sample type influence, mainly through MGEs, the profile and dispersion of ARGs in pig production. Video Abstract.

Occurrence and faecal shedding of extended-spectrum beta-lactamase-producing Escherichia coli in sows and their offspring

The aim of the present study was to monitor the presence of extended-spectrum beta-lactamase (ESBL) producing E. coli on farm A with the history of previous use of ceftiofur in suckling pigletsand to analyse the risk factors of selection and dissemination of ESBL producers in the production herd. In the year of 2014, a total of 411 samples (rectal swabs or faeces)from pigs of various age categories (sows, gilts and suckling piglets) were collected. The sampling was performed more than 24 months after the ban of ceftiofur on the farm.The sows and gilts were sampled repeatedly before and after farrowing. All collected samples were directly cultivated on MacConkey agar (MCA) containing cefotaxime (2 mg/l) and obtained sub-cultures were tested for ESBL production by double disc synergy test. According to our results, all gilts were negative for ESBL-producing E. coli in the introduction period, however, the excretion of ESBL-producing E. coli was observed before and after delivery. Most of the new-born piglets from positive sows and gilts shed ESBL-producing E. coli early after birth. All tested ESBL-producing isolates were resistant to multiple antimicrobials, suggesting that antibiotics from other groups used for therapy co-select for ESBL producers in pigs on the studied farm. Intestinal colonization of lactating sows and their offspring as well as survival of ESBL-producing E. coli in the farm environment should be recognised as important risk factors of circulation and long-time persistence of ESBL producers in the herd.

Extended Spectrum β-Lactamase (ESBL) Producing Escherichia coli in Pigs and Pork Meat in the European Union

The aim of this article is to review the fast and worldwide distribution of ESBL enzymes and to describe the role of the pork production chain as a reservoir and transmission route of ESBL-producing Escherichia coli and ESBLs in the European Union (EU). The use of β-lactam antibiotics in swine production and the prevalence of ESBL producing E. coli in fattening pigs and pork meat across Europe is analyzed. Overall, an increasing trend in the prevalence of presumptive ESBL producing E. coli in fattening pigs in the EU has been observed in the last decade, although with major differences among countries, linked to different approaches in the use of antimicrobials in pork production within the EU. Moreover, the various dissemination pathways of these bacteria along the pork production chain are described, along with factors at farm and slaughterhouse level influencing the risk of introducing or spreading ESBL producing bacteria throughout the food chain.

Foraging at Solid Urban Waste Disposal Sites as Risk Factor for Cephalosporin and Colistin Resistant Escherichia coli Carriage in White Storks (Ciconia ciconia)

White stork (Ciconia ciconia) may act as a reservoir and vehicle of cephalosporin resistant (CR) Escherichia coli. Between 2011 and 2014, we sampled white storks from colonies exposed to different degrees of anthropic pressure across the major areas of natural distribution of white storks in Spain. Cloacal swab samples (n = 467) were obtained from individuals belonging to 12 different colonies from six different regions. Additionally, 70 samples were collected from recently deposited droppings at the base of nesting platforms. We phenotypically characterized E. coli isolates, confirmed presence of CR genes and classified plasmids. Risk factors for acquiring these genes were assessed. Overall, 8.8% (41 out of 467) storks carried CR E. coli in their cloaca and five (7.1%) were identified from recently deposited droppings; therefore, 46 isolates were further characterized. Of them, 20 contained bla_CTX–M–1, nine bla_CMY–2, six bla_CTX–M–14, four bla_SHV–12, three bla_CTX–M–15, two bla_CTX–M–32, one bla_CTX–M–1 together with bla_CMY–2, and one bla_CTX–M–1 together with bla_SHV–12. All were multidrug-resistant, and four harbored the plasmid-mediated colistin resistance mcr-1 gene. CR genes were associated with the presence of IncI1, IncFIB, and IncN replicon families. XbaI-macrorestriction analysis revealed a great diversity among most of the XbaI-PFGE types, but indistinguishable types were also seen with isolates obtained from different locations. Clonal complex 10 was the most common among CR E. coli and two bla_CTX–M–15 positive isolates were identified as B2-ST131. Carriage of CR E. coli was significantly higher in colonies located close to solid urban waste disposal sites in which foraging on human waste was more likely and in one case to cattle grazing. The co-occurrence of bla_CMY–2 and mcr-1 on plasmids of E. coli isolated from wild birds as early as 2011 is of note, as the earliest previous report of mcr-1 in wild birds is from 2016. Our study shows that foraging at landfills and in association with cattle grazing are important risk factors for the acquisition of CR E. coli in white storks.

Recent advances in the development of β-lactamase inhibitors

β-Lactam antibiotics are the most commonly prescribed antibiotics worldwide; however, antimicrobial resistance (AMR) is a global challenge. The β-lactam resistance in Gram-negative bacteria is due to the production of β-lactamases, including extended-spectrum β-lactamases, metallo-β-lactamases, and carbapenem-hydrolyzing class D β-lactamases. To restore the efficacy of BLAs, the most successful strategy is to use them in combination with β-lactamase inhibitors (BLI). Here we review the medically relevant β-lactamase families and penicillins, diazabicyclooctanes, boronic acids, and novel chemical scaffold-based BLIs, in particular approved and under clinical development.

Prevalence of Cefotaxime-Resistant Escherichia coli Isolates from Healthy Cattle and Sheep in Northern Spain: Phenotypic and Genome-Based Characterization of Antimicrobial Susceptibility

In order to estimate herd-level prevalence of extended-spectrum β-lactamase/AmpC β-lactamase (ESBL/AmpC)- and carbapenemase-producing commensal Escherichia coli in ruminants in the Basque Country (northern Spain), a cross-sectional survey was conducted in 2014 to 2016 in 300 herds using selective isolation. ESBL-/AmpC-producing E. coli was isolated in 32.9% of dairy cattle herds, 9.6% of beef cattle herds, and 7.0% of sheep flocks. No carbapenemase-producing E. coli was isolated. Phenotypic antimicrobial susceptibility determined by broth microdilution using EUCAST epidemiological cutoff values identified widespread coresistance to extended-spectrum cephalosporins and other antimicrobials (110/135 isolates), particularly tetracycline, sulfamethoxazole, trimethoprim, and ciprofloxacin. All isolates were susceptible to tigecycline, imipenem, meropenem, and colistin. The genomes of 66 isolates were sequenced using an Illumina NovaSeq 6000 and screened for antimicrobial resistance determinants against ResFinder and PointFinder. The plasmid/chromosomal locations of resistance genes were predicted with PlasFlow, and plasmid replicons were identified using PlasmidFinder. Fifty-two acquired resistance genes and point mutations in another four genes that coded for resistance to 11 antimicrobial classes were identified. Fifty-five genomes carried ESBL-encoding genes, bla _CTX-M-14 being the most common, and 11 carried determinants of the AmpC phenotype, mostly the bla _CMY-2 gene. Additionally, genes coding for β-lactamases of the CTX-M group 9 were detected as well as the sporadic presence of bla _SHV-12, bla _CMY-4, and a point mutation in the ampC promoter. Only a bovine isolate coharbored more than one ESBL/AmpC genetic determinant (bla _CTX-M-14 and a mutation in the ampC promoter), confirming its ESBL- and AmpC β-lactamase-producing phenotype. Most ESBL/AmpC genes were located in IncI1 plasmids, which also carried a great variety of other antimicrobial resistance genes.IMPORTANCE Extended-spectrum β-lactamase (ESBL)- and AmpC β-lactamase (AmpC)-producing E. coli isolates have emerged in recent years as some of the fastest spreading antimicrobial resistance determinants in humans and food-producing animals, becoming a concern for animal and public health. This study provided insight into the prevalence of cefotaxime-resistant E. coli in cattle and sheep in the Basque Country and the associated genetic determinants of antimicrobial resistance. These constituted an important contribution to the limited repository of such data for cattle in the region and for sheep worldwide. Antimicrobial susceptibility testing by phenotypic and molecular methods is key in surveillance programs to enhance early detection of resistance development, monitor resistance trends, and provide guidance to clinicians in selecting the adequate therapy.

Characteristics of Extended-Spectrum β-Lactamase-Producing Escherichia coli From Dogs and Cats Admitted to a Veterinary Teaching Hospital in Taipei, Taiwan From 2014 to 2017

Extended-spectrum β-lactamases (ESBLs) are enzymes that mediate resistance to newer β-lactam antibiotics, including extended-spectrum cephalosporins and monobactams. The production of ESBL is primarily plasmid mediated, and such plasmids often comprise the genes that encode resistance to other classes of antimicrobials, such as aminoglycosides and fluoroquinolones. Therefore, ESBL-producing microorganisms leave clinicians with limited therapeutic options in both human and veterinary medicine. Compared with human medicine, information regarding ESBL-producing microorganisms is limited in veterinary medicine. We screened for ESBL-producing Escherichia coli in dogs and cats admitted to National Taiwan University Veterinary Hospital, Taipei, from 2014 to 2017 and further analyzed the genotypes and phylogenetic traits of these ESBL producers. Double disk tests specified by the Clinical and Laboratory Standards Institute were performed on 283 E. coli isolates and revealed a total of 65 E. coli (54 from dogs and 11 from cats) with the ESBL phenotype (22.8%). bla_{CTX−M−1group} and bla_{CTX−M−2group} were the most commonly identified ESBL gene groups. bla_CTX−M−55 was the main ESBL gene within the bla_{CTX−M−1group}, whereas the bla_{CTX−M−2group} contained only bla_{CTX−M−124}. The ESBL-producing E. coli were all resistant to ampicillin. The resistance rate to ceftiofur, doxycycline, enrofloxacin, and ciprofloxacin was 93.8, 73.8, 80, and 78.5%, respectively. Of the antibiotics tested, greater sensitivity to imipenem and gentamicin was noted. Multilocus sequence typing indicated that ST457, ST131, and ST648 were the most common sequence types. Our study identified eight ST131/O25b isolates, which is a global zoonotic clone of public health concern. The major ESBL genes of these clones were bla_{CTX−M−174} and bla_{CTX−M−194}. Because companion animals such as dogs and cats are in close contact with humans, the characterization of ESBL producers originating from them is crucial from the perspective of both public health and veterinary medicine.

Characterisation of Porcine Enteropathogenic Escherichia Coli Isolated in Northeastern India

Introduction

Enteropathogenic Escherichia coli (EPEC) is one of the main pathotypes causing gastroenteritis, particularly in young immunocompromised hosts. The study reports the prevalence, characterisation, and molecular epidemiology of EPEC from piglets in northeastern India.

Material and Methods

A total of 457 faecal samples were collected, from which 1,286 E. coli strains were isolated and screened by PCR. The resultant EPEC strains were serotyped and phenotypically characterised for resistance against 15 antimicrobials. Also, the phylogenetic sequence was analysed for 11 selected strains.

Results

A total of 42 strains (3.26%) belonged to atypical EPEC, of which, 15 (35.71%, and 2.29% of the 654 strains from this farm type) were isolated from organised and 27 (64.29%, and 4.27% of the 632 strains from this farm type) from unorganised farms; further, 5 (11.90% of the EPEC strains and 1.51% of the 330 strains from this breed) were isolated from the indigenous breeds and 37 (88.10%, and 3.87% of the 956 strains from this breed) from crossbred piglets. Serogroups O111 (11.9%) and O118 (7.14%) were the most prevalent of the 10 present. Sequence analysis of a length of the eaeA gene of 11 isolates of the region showed them to have 100% homology with each other and their identity ranged from 99.4% to 99.7% with GenBank reference sequences. All the EPEC isolates were multi-drug resistant, showing the highest resistance to amoxicillin (80.9%) and cephalexin (76.19%).

Conclusion

The study highlighted the association of EPEC with piglet’s diarrhoea in northeastern India. EPEC isolates belonged to many serotypes and phenotypically all were multi-drug resistant with close genetic homology.

Human faeces-associated extended-spectrum β-lactamase-producing Escherichia coli discharge into sanitation systems in 2015 and 2030: a global and regional analysis

BACKGROUND

Improving management of and treatment within sanitation waste streams could slow the development and transmission of antimicrobial-resistant organisms, but the magnitude of impact has not been quantified. Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are a major cause of antimicrobial-resistant infections and are frequently detected in faecal waste streams, making them model indicators of the distribution of antimicrobial-resistant organisms that are transmitted through the faecal-oral route. We aimed to estimate the mass of faeces containing ESBL-producing E coli entering different levels of the sanitation ladder globally and by WHO region to determine the global scale at which sanitation infrastructure serves as a vehicle for dissemination of antimicrobial-resistant organisms.

METHODS

In this global and regional analysis, we used publicly available sanitation coverage data from the WHO/UNICEF Joint Monitoring Programme and most recent available scientific literature on human faecal production (2018) and carriage of ESBL-producing E coli by healthy individuals (2016) to estimate the quantity of faeces that has been discharged that contains ESBL-producing E coli for 2015 and projected for 2030. We estimated the mass of faeces containing ESBL-producing E coli by WHO region and at different levels of the Sustainable Development Goal sanitation ladder-ie, into at-least basic (ie, safely managed or basic) systems, limited systems, and unimproved systems, and via open defecation. We modelled three scenarios in which the proportion of ESBL-producing E coli among all E coli that was excreted by carriers varied on the basis of the scientific literature: 100% (scenario A), 10% (scenario B), or 1% (scenario C).

FINDINGS

Under scenario B, we estimated that approximately 19 billion kg of faeces carrying ESBL-producing E coli was excreted in 2015 globally. Approximately 65·8% (1·2-120 billion kg depending on modelled scenario) of this faecal biomass was managed in at-least basic sanitation systems, 8·4% (160 million-16 billion kg) in limited sanitation systems, 14·4% (270 million-27 billion kg) in unimproved sanitation systems, and 11·4% (220 million-22 billion kg) was openly defecated. The regions with the highest proportion of openly defecated faeces containing ESBL-producing E coli were the South-East Asia (29·4%) and African (21·8%) regions. The South-East Asia, Western Pacific, and African regions produced 524 billion kg (63%) of the total global human faecal biomass, but 16·9 billion kg (90%) of faeces containing ESBL-producing E coli under scenario B. By 2030, estimates under scenario B will have approximately doubled to 37·6 billion kg of faeces carrying ESBL-producing E coli under the most conservative projections.

INTERPRETATION

At-least basic sanitation does not guarantee effective removal or inactivation of antimicrobial-resistant organisms from faecal biomass. However, our findings indicate the need for mitigating transport of antimicrobial-resistant organisms via sanitation systems that are not safely managed, including open defecation, which might result in direct environmental discharge and subsequent risk of transmission back to humans.

FUNDING

None.