Molecular survey of mcr1 and mcr2 plasmid mediated colistin resistance genes in Escherichia coli isolates of animal origin in Iran

Investigation of Antibiotic Resistance of E. coli Associated with Farm Animal Feces with Participation of Citizen Scientists

This paper presents the findings of a large-scale study on antibiotic resistance in bacteria found in farm animal feces across Russia. The study included 6578 samples of farm animal manure from 13 regions in Russia, with the help of citizen scientists. Molecular and microbiological methods were used to analyze 1111 samples of E. coli. The microbiological analysis focused on culturing the microorganisms present in the fecal samples on selective media for E. coli and evaluating the sensitivity of the bacteria to different antibiotics, including ampicillin, tetracycline, chloramphenicol, cefotaxime, and ciprofloxacin. The molecular analysis involved isolating the genomic DNA of the bacteria and conducting PCR assays to detect the vanA, vanB, and mcr-1 antibiotic resistance genes. The results demonstrated significant differences in antibiotic sensitivity of the samples that are morphologically identical to E. coli from different regions. For example, 98.0% and 82.5% of E. coli and other fecal bacterial isolates from the Omsk and Vologda regions lacked antibiotic resistance genes, while 97.7% of samples from the Voronezh region possessed three resistance genes simultaneously. The phenotypic antibiotic sensitivity test also revealed regional differences. For instance, 98.1% of fecal bacterial samples from cattle in the Udmurt Republic were sensitive to all five antibiotics tested, whereas 92.8% of samples from the Voronezh region showed resistance to all five antibiotics. The high level of antibiotic resistance observed may be attributed to their use in farming practices. The distinctive feature of our research is that comprehensive geographical coverage was achieved by using a citizen science platform. Citizen scientists, specifically students from colleges and universities, were responsible for the collection and initial analysis of samples. The project attracted 3096 student participants, enabling the collection and analysis of a significant number of samples from various locations in Russia.

Investigating the virulence-associated genes and antimicrobial resistance of Escherichia fergusonii Isolated from diseased ostrich chicks

This study investigates the presence of virulence-associated genes and antimicrobial resistance (AMR) in Escherichia fergusonii isolates obtained from ostrich chicks. A total of 287 isolates were recovered from 106 fecal samples from ostrich chicks suffering from diarrhea and subjected to molecular identification and biochemical characterization. E. fergusonii was detected in 10 samples (9.4 %) using two PCR-detection protocols. Notably, the isolates lacked various virulence genes commonly associated with pathogenic E. coli including elt, est, stx, eae, ehly, cdt, iss, iutA, iroN, hlyA, ompT, except for one isolate harboring the astA gene. Antimicrobial susceptibility testing revealed that all isolates were susceptible to ciprofloxacin, while high resistance was observed against amoxicillin clavulanate (AMC), trimethoprim-sulfamethoxazole (SXT), and doxycycline (D). Moreover, eight isolates displayed multidrug resistance (MDR) and four exhibited resistance to 9-11 antimicrobials. The most frequent resistance gene was sul2, which was present in all isolates; the other resistance genes detected consisted of int1 (4/10), int2 (3/10), blaCMY (2/10), and qnrS, blaTEM, blaCMY, blaCTX-M, and flo each were detected only in one E. fergusonii Isolate. Plasmid replicon typing identified the presence of I1 (7/10), N (5/10), and Y (1/10). This study provides valuable insights into the virulence and antimicrobial resistance of E. fergusonii isolates from ostrich chicks, highlighting the complexity of antimicrobial resistance mechanisms exhibited by these bacteria. Further research is essential to understand the transmission dynamics and clinical implications of these findings in veterinary and public health settings.

Evaluation of in-feed supplementation of formic acid and thymol as non-antibiotic growth promoters and assessing their effect on antimicrobial resistant E.coli isolated in Turkey

With the rampant usage of antibiotics as growth promoters (AGPs) in poultry sector, there has been alarming concerns of antimicrobial resistant microbes such as Escherichia coli. Diversification of poultry farming due to consumer demand for safer products with higher protein content, turkey production is gaining popularity. Feed additives such as formic acid (FA) and thymol (TH) are effectively replacing AGPs due to their antimicrobial action. This directed the researchers to find alternatives to antibiotics such as thymol and formic acid because of their strong antimicrobial, anti-oxidative, digestive-stimulating properties. To assess the efficacy of FA and TH as growth promoters and their effect on the antimicrobial resistance (AMR) load, the current study (0-12 weeks) was conducted in CARI VIRAT turkey poults (n = 256; unsexed) those were randomly distributed into eight treatment groups: control(T1), AGP (T2), graded levels of FA (T3 to T5) @ 2.5, 5 and 7.5 ml/kg and TH (T6 to T8) @ 120, 240 and 350 mg/kg. Cloacal swab samples were collected at 0, 4th, 8th and 12th week interval and processed further for isolation, identification and assessment of resistance profile of E. coli. The final body weight, cumulative gain and FCR were significantly (p < 0.05) better for birds under supplementation. The Total plate count (TPC) and coliforms showcased a significant (p < 0.001) reduction in the FA and TH supplement groups as compared to control and AGP group. The resistance profile indicated E. coli isolates from AGP group with significantly (p < 0.001) highest resistivity against antibiotics (viz. chloramphenicol, tetracycline, nalidixic acid, chlortetracycline) while isolates from FA (T5) and TH (T8) groups were the least resistant. blaAmpC gene was significantly (p < 0.001) harbored in T2 isolates whereas least detected in T5 and T8. It was inferred that formic acid (7.5 ml/kg) and thymol (360 mg/kg) can effectively replace AGPs and lower AMR burden in poultry.

Frequencies of mobilized colistin resistance (mcr-1, 2) genes in clinically isolated Escherichia coli; a cross sectional study

OBJECTIVE

Escherichia coli (E. coli) is an opportunistic bacterium, which is globally recognized for its high prevalence and antimicrobial resistance (AMR). The presence of colistin-resistant representative mcr- 1, 2 genes in multi-drug resistant (MDR) clinically isolated E. coli is the main goal of this survey. After biochemically and molecular confirmation tests, susceptibility testing, biofilm formation, and minimum inhibitory concentration to colistin were performed on 100 E. coli isolates. Subsequently, taking advantage of uniplex-PCR, the presence of some responsible genes (mcr- 1, mcr- 2) to colistin-resistant phenotypes in mentioned bacterium was assessed.

RESULTS

Disc diffusion methods indicated that the highest resistance rate was against ampicillin (80.0%), and trimethoprim/sulfamethoxazole (63%). Among the E. coli isolates, 72 (72.0%) was determined as MDR, respectively. Moreover, 47 (47%) strains were determined as extreme beta-lactamase (ESBL) phenotypes. Among 41 slime-producing E. coli strains, 7 (17.07%), 14 (34.14%), and 20 (48.78%) strains exhibited high, moderate, and weak levels of biofilm formation, respectively. Fifty-nine (81.94%), and 1(100%) of MDR isolates were assessed as colistin resistant (MIC > 2) and susceptible (MIC ≤ 2) as well. In 26(36.11%) of colistin-resistant isolates and 1(1.38%) of colistin, susceptible isolate mcr-1 gene was found. There is no mcr- 2 gene was detected in isolates.

CONCLUSION

The diversity of high antibiotic-resistant rates could be avoided by developing appropriate healthcare policies and community awareness. Alarming resistance rates were observed in colistin and ampicillin, which should be taken into account in therapy guidelines.

Mobile Colistin Resistance (mcr) Gene-Containing Organisms in Poultry Sector in Low- and Middle-Income Countries: Epidemiology, Characteristics, and One Health Control Strategies

Mobile colistin resistance (mcr) genes (mcr-1 to mcr-10) are plasmid-encoded genes that threaten the clinical utility of colistin (COL), one of the highest-priority critically important antibiotics (HP-CIAs) used to treat infections caused by multidrug-resistant and extensively drug-resistant bacteria in humans and animals. For more than six decades, COL has been used largely unregulated in the poultry sector in low- and middle-income countries (LMICs), and this has led to the development/spread of mcr gene-containing bacteria (MGCB). The prevalence rates of mcr-positive organisms from the poultry sector in LMICs between January 1970 and May 2023 range between 0.51% and 58.8%. Through horizontal gene transfer, conjugative plasmids possessing insertion sequences (ISs) (especially ISApl1), transposons (predominantly Tn6330), and integrons have enhanced the spread of mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, mcr-7, mcr-8, mcr-9, and mcr-10 in the poultry sector in LMICs. These genes are harboured by Escherichia, Klebsiella, Proteus, Salmonella, Cronobacter, Citrobacter, Enterobacter, Shigella, Providencia, Aeromonas, Raoultella, Pseudomonas, and Acinetobacter species, belonging to diverse clones. The mcr-1, mcr-3, and mcr-10 genes have also been integrated into the chromosomes of these bacteria and are mobilizable by ISs and integrative conjugative elements. These bacteria often coexpress mcr with virulence genes and other genes conferring resistance to HP-CIAs, such as extended-spectrum cephalosporins, carbapenems, fosfomycin, fluoroquinolone, and tigecycline. The transmission routes and dynamics of MGCB from the poultry sector in LMICs within the One Health triad include contact with poultry birds, feed/drinking water, manure, poultry farmers and their farm workwear, farming equipment, the consumption and sale of contaminated poultry meat/egg and associated products, etc. The use of pre/probiotics and other non-antimicrobial alternatives in the raising of birds, the judicious use of non-critically important antibiotics for therapy, the banning of nontherapeutic COL use, improved vaccination, biosecurity, hand hygiene and sanitization, the development of rapid diagnostic test kits, and the intensified surveillance of mcr genes, among others, could effectively control the spread of MGCB from the poultry sector in LMICs.

Farm to table: colistin resistance hitchhiking through food

Colistin is a high priority, last-resort antibiotic recklessly used in livestock and poultry farms. It is used as an antibiotic for treating multi-drug resistant Gram-negative bacterial infections as well as a growth promoter in poultry and animal farms. The sub-therapeutic doses of colistin exert a selection pressure on bacteria leading to the emergence of colistin resistance in the environment. Colistin resistance gene, mcr are mostly plasmid-mediated, amplifying the horizontal gene transfer. Food products such as chicken, meat, pork etc. disseminate colistin resistance to humans through zoonotic transfer. The antimicrobial residues used in livestock and poultry often leaches to soil and water through faeces. This review highlights the recent status of colistin use in food-producing animals, its association with colistin resistance adversely affecting public health. The underlying mechanism of colistin resistance has been explored. The prohibition of over-the-counter colistin sales and as growth promoters for animals and broilers has exhibited effective stewardship of colistin resistance in several countries.

Occurrence of mcr-1 and mcr-2 colistin resistance genes in porcine Escherichia coli isolates (2010-2020) and genomic characterization of mcr-2-positive E. coli

Introduction

The global emergence of plasmid-mediated colistin resistance is threatening the efficacy of colistin as one of the last treatment options against multi-drug resistant Gram-negative bacteria. To date, ten mcr-genes (mcr-1 to mcr-10) were reported. While mcr-1 has disseminated globally, the occurrence of mcr-2 was reported scarcely.

Methods and results

We determined the occurrence of mcr-1 and mcr-2 genes among Escherichia coli isolates from swine and performed detailed genomic characterization of mcr-2-positive strains. In the years 2010-2017, 7,614 porcine E. coli isolates were obtained from fecal swine samples in Europe and isolates carrying at least one of the virulence associated genes predicting Shiga toxin producing E. coli (STEC), enterotoxigenic E. coli (ETEC) or enteropathogenic E. coli (EPEC) were stored. 793 (10.4%) of these isolates carried the mcr-1 gene. Of 1,477 additional E. coli isolates obtained from sheep blood agar containing 4 mg/L colistin between 2018 and 2020, 36 (2.4%) isolates were mcr-1-positive. In contrast to mcr-1, the mcr-2 gene occurred at a very low frequency (0.13%) among the overall 9,091 isolates. Most mcr-2-positive isolates originated from Belgium (n = 9), one from Spain and two from Germany. They were obtained from six different farms and revealed multilocus sequence types ST10, ST29, ST93, ST100, ST3057 and ST5786. While the originally described mcr-2.1 was predominant, we also detected a new mcr-2 variant in two isolates from Belgium, which was termed mcr-2.8. MCR-2 isolates were mostly classified as ETEC or ETEC-like, while one isolate from Spain represented an atypical enteropathogenic E. coli (aEPEC; eae+). The ST29-aEPEC isolate carried mcr-2 on the chromosome. Another eight isolates carried their mcr-2 gene on IncX4 plasmids that resembled the pKP37-BE MCR-2 plasmid originally described in Belgium in 2015. Three ST100 E. coli isolates from a single farm in Belgium carried the mcr-2.1 gene on a 47-kb self-transmissible IncP type plasmid of a new IncP-1 clade.

Discussion

This is the first report of mcr-2 genes in E. coli isolates from Germany. The detection of a new mcr-2 allele and a novel plasmid backbone suggests the presence of so far undetected mcr-2 variants and mobilizable vehicles.

Prevalence of main quinolones and carbapenems resistance genes in clinical and veterinary Escherichia coli strains

Background and Objectives

Antibiotics-resistant Escherichia coli strains are considered one of the most important causes of human and animal infections worldwide. The aim of current study was to detect common resistance (carbapenems and quinolones) genes by PCR.

Materials and Methods

A total of 100 E. coli strains isolated from human urinary tract infection and 20 isolated strains of aborted sheep embryos were collected. PCR was performed using specific primers to detect the resistance genes.

Results

Overall, among the quinolones resistance genes, qnrS resistance gene had the highest frequency (48%) and among carbapenem resistance genes, imp resistance gene had the highest frequency (45%). The frequency of resistance genes, IMP (28.45%), KPC (9.5%), VIM (9.15%), NDM (7.20%) were observed in clinical and veterinary strains, respectively. According to the results, 38.6% of E. coli strains had at least one from five genes of resistance to quinolones. The lowest frequency of resistance gene was related to qnrA, which was observed in only 29 (24.2%) strains.

Conclusion

Monitoring of carbapenem and quinolone resistance in pathogenic E. coli to humans and animals has an important value in revising treatment guidelines and the national public health, and plays an important role in preventing the spread of resistant strains.

Detection of Colistin Sulfate on Piglet Gastrointestinal Tract Microbiome Alterations

The gut microbiome exerts important functions on host health maintenance, whereas excessive antibiotic use may cause gut flora dysfunction resulting in serious disease and dysbiosis. Colistin is a broad-spectrum antibiotic with serious resistance phenomena. However, it is unclear whether colistin alters the gastrointestinal tract microbiome in piglets. In this study, 16s rDNA-based metagenome analyses were used to assess the effects of colistin on the modification of the piglet microbiome in the stomach, duodenum, jejunum, cecum, and feces. Both α- and β-diversity indices showed that colistin modified microbiome composition in these gastrointestinal areas. In addition, colistin influenced microbiome composition at the phylum and genus levels. At the species level, colistin upregulated Mycoplasma hyorhinis, Chlamydia trachomatis, Lactobacillus agilis, Weissella paramesenteroides, and Lactobacillus salivarius abundance, but downregulated Actinobacillus indolicus, Campylobacter fetus, Glaesserella parasuis, Moraxella pluranimalium, Veillonella caviae, Neisseria dentiae, and Prevotella disiens abundance in stomachs. Colistin-fed piglets showed an increased abundance of Lactobacillus mucosae, Megasphaera elsdenii DSM 20460, Fibrobacter intestinalis, and Unidentified rumen bacterium 12-7, but Megamonas funiformis, Uncultured Enterobacteriaceae bacterium, Actinobacillus porcinus, Uncultured Bacteroidales bacterium, and Uncultured Clostridiaceae bacterium abundance was decreased in the cecum. In feces, colistin promoted Mucispirillum schaedleri, Treponema berlinense, Veillonella magna, Veillonella caviae, and Actinobacillus porcinus abundance when compared with controls. Taken together, colistin modified the microbiome composition of gastrointestinal areas in piglets. This study provides new clinical rationalization strategies for colistin on the maintenance of animal gut balance and human public health.

Screening of colistin-resistant bacteria in livestock animals from France

Colistin is frequently used as a growth factor or treatment against infectious bacterial diseases in animals. The Veterinary Division of the European Medicines Agency (EMA) restricted colistin use as a second-line treatment to reduce colistin resistance. In 2020, 282 faecal samples were collected from chickens, cattle, sheep, goats, and pigs in the south of France. In order to track the emergence of mobilized colistin resistant (mcr) genes in pigs, 111 samples were re-collected in 2021 and included pig faeces, food, and water from the same location. All samples were cultured in a selective Lucie Bardet Jean-Marc Rolain (LBJMR) medium and colonies were identified using MALDI-TOF mass spectrometry and then antibiotic susceptibility tests were performed. PCR and Sanger sequencing were performed to screen for the presence of mcr genes. The selective culture revealed the presence of 397 bacteria corresponding to 35 different bacterial species including Gram-negative and Gram-positive. Pigs had the highest prevalence of colistin-resistant bacteria with an abundance of intrinsically colistin-resistant bacteria and from these samples one strain harbouring both mcr-1 and mcr-3 has been isolated. The second collection allowed us to identify 304 bacteria and revealed the spread of mcr-1 and mcr-3 in pigs. In the other samples, naturally, colistin-resistant bacteria were more frequent, nevertheless the mcr-1 variant was the most abundant gene found in chicken, sheep, and goat samples and one cattle sample was positive for the mcr-3 gene. Animals are potential reservoir of colistin-resistant bacteria which varies from one animal to another. Interventions and alternative options are required to reduce the emergence of colistin resistance and to avoid zoonotic transmissions.

Distribution and model prediction of antibiotic resistance genes in Weishan Lake based on the indication of Chironomidae larvae

The widespread contamination of antibiotic resistance genes (ARGs) in freshwater environment are becoming a serious challenge to human health and ecological safety. Rapid and efficient monitoring of ARGs pollution is of great significance to ARGs control. Water, bottom mud, and fish have all been used to indicate ARG contamination in aquatic environments. However, it is unclear whether macrobenthic invertebrates in the food chain of aquatic environments can be indicators of ARG contamination. In this study, we demonstrated that ARGs including tetA gene, sul2 gene, and km gene were distributed in Chironomidae larvae in Weishan Lake. The ARG distribution was related to animal species, body parts, sampling sites, time, urban environment, animal farming, south-to-north water diversion, food chain, antibiotics, and water storage. Mathematical model predictions of ARG contamination in Weishan Lake were constructed based on the structural equation model (SEM) and the distribution of ARG sul2 in Chironomidae larvae. Influencing factors such as water storage, metal elements, antibiotic, and temperature were found to be closely related to the prediction of ARG contamination. This study provided a new indicator for ARG contamination in freshwater environments and a method to predict ARGs contamination.

Chironomidae larvae: A neglected enricher of antibiotic resistance genes in the food chain of freshwater environments

Infection caused by pathogenic bacteria carrying antibiotic resistance genes (ARGs) is a serious challenge to human health. Water environment, including water and surface sediments, is an important repository of ARGs, and the activity of aquatic animal can affect the development of ARG pollution in the water environment. Macrobenthic invertebrates are an important component of aquatic ecosystems, and their effects on ARG development in aquatic environments remain unreported. The distribution of ARGs, including tetA gene, sul2 gene, and kan gene, in Chironomidae larvae is demonstrated in this study for the first time. The ARG distribution was related to sampling points, metal elements, and seasons. Animal models demonstrated that Chironomidae larvae enriched ARGs from water and passed them on to downstream predators in the food chain. Conjugative transfer mediated by resistant plasmids was crucial in the spread of ARG in Chironomidae larvae, and upregulated expression of trfAp gene and trbBp gene was the molecular mechanism. Escherichia in Proteobacteria and Flavobacterium in Bacteroidetes, which are gram-negative bacteria in Chironomidae larvae, are the primary host bacteria of ARGs confirmed via resistance screening and DNA sequencing of V4 region of 16S rRNA gene. Feeding experiments further confirmed that ARGs from Chironomidae larvae can be enriched in the fish gut. Research gaps in food chain between sediments and fish are addressed in this study, and Chironomidae larvae is an important enricher of ARGs in the freshwater environment.

Characteristics of colistin-resistant Escherichia coli from pig farms in Central China

The emergence and dissemination of colistin resistance in Enterobacteriaceae mediated by plasmid-borne mcr genes in recent years now pose a threat to public health. In this study, we isolated and characterized colistin-resistant and/or mcr-positive E. coli from pig farms in Central China. Between 2018 and 2019, 594 samples were collected and recovered 445 E. coli isolates. Among them, 33 with colistin resistance phenotypes and 37 that were positive for mcr genes were identified, including 34 positive for mcr-1, one positive for mcr-3, and two positive for both mcr-1 and mcr-3. An insertion of nine bases (“CTGGATACG”) into mcr-1 in four mcr-positive isolates led to gene dysfunction, and therefore did not confer the colistin resistance phenotype. Antimicrobial susceptibility testing revealed that 37 mcr-positive isolates showed severe drug resistance profiles, as 50% of them were resistant to 20 types of antibiotics. Multilocus sequence typing revealed a heterogeneous group of sequence types in mcr-positive isolates, among which ST10 (5/37), ST156 (5/37), and ST617 (4/37) were the predominant types. Plasmid conjugation assays showed that mcr-carrying plasmids of 25 mcr-positive isolates were conjugated with E. coli recipient, with conjugation frequencies ranging from 1.7 × 10-6 to 4.1 × 10-3 per recipient. Conjugation of these mcr genes conferred a colistin resistance phenotype upon the recipient bacterium. PCR typing of plasmids harbored in the 25 transconjugants determined six types of plasmid replicons, including IncX4 (14/25), FrepB (4/25), IncI2 (3/25), IncHI2 (2/25), FIB (1/25), and IncI1 (1/25). This study contributes to the current understanding of antibiotic resistance and molecular characteristics of colistin-resistant E. coli in pig farms.