A Study of the Transfer of Tetracycline Resistance Genes Between Escherichia coli in the Intestinal Tract of a Mouse and a Chicken Model

Soil-specific responses in the antibiotic resistome of culturable Acinetobacter spp. and other non-fermentative Gram-negative bacteria following experimental manure application

Acinetobacter spp. and other non-fermenting Gram-negative bacteria (NFGNB) represent an important group of opportunistic pathogens due to their propensity for multiple, intrinsic, or acquired antimicrobial resistance (AMR). Antimicrobial resistant bacteria and their genes can spread to the environment through livestock manure. This study investigated the effects of fresh manure from dairy cows under antibiotic prophylaxis on the antibiotic resistome and AMR hosts in microcosms using pasture soil. We specifically focused on culturable Acinetobacter spp. and other NFGNB using CHROMagar Acinetobacter. We conducted two 28-days incubation experiments to simulate natural deposition of fresh manure on pasture soil and evaluated the effects on antibiotic resistance genes (ARGs) and bacterial hosts through shotgun metagenomics. We found that manure application altered the abundance and composition of ARGs and their bacterial hosts, and that the effects depended on the soil source. Manure enriched the antibiotic resistome of bacteria only in the soil where native bacteria had a low abundance of ARGs. Our study highlights the role of native soil bacteria in modulating the consequences of manure deposition on soil and confirms the potential of culturable Acinetobacter spp. and other NFGNB to accumulate AMR in pasture soil receiving fresh manure.

Prevalence of Antibiotic-Resistant E. coli Strains in a Local Farm and Packing Facilities of Honeydew Melon in Hermosillo, Sonora, Mexico

Pathogenic strains of Escherichia coli threaten public health due to their virulence factors and antibiotic resistance. Additionally, the virulence of this bacterium varies by region depending on environmental conditions, agricultural practices, and the use of antibiotics and disinfectants. However, there is limited research on the prevalence of antibiotic-resistant E. coli in agriculture. Therefore, this research aimed to determine the antibiotic resistance of E. coli isolated from the Honeydew melon production system in Hermosillo, Sonora, Mexico. Thirty-two E. coli strains were isolated from 445 samples obtained from irrigation water, harvested melons, the hands of packaging workers, boxes, and discarded melons. The resistance profile of the E. coli strains was carried out to 12 antibiotics used in antimicrobial therapeutics against this bacterium; a high level of resistance to ertapenem (100%) was detected, followed by meropenem (97%), and ampicillin (94%); 47% of the strains were classified as multidrug-resistant. It was possible to identify the prevalence of the extended-spectrum β-lactamase (ESBLs) gene bla_TEM (15.6%), as well as the non-ESBL genes qepA (3.1%) and aac(6')lb-cr (3.1%). The E. coli strains isolated from irrigation water were significantly associated with resistance to aztreonam, cefuroxime, amikacin, and sulfamethoxazole/trimethoprim. Irrigation water, packing workers' hands, and discarded melons showed a higher prevalence of antibiotic-resistant, ESBL, and non-ESBL genes of E. coli strains in a farm and packing facility of Honeydew melon in Hermosillo, Sonora.

Assessing the Impact of Heat Treatment of Food on Antimicrobial Resistance Genes and Their Potential Uptake by Other Bacteria-A Critical Review

The dissemination of antibiotic resistance genes (ARGs) is a global health concern. This study identifies and critically reviews the published evidence on whether cooking (heating) food to eliminate bacterial contamination induces sufficient damage to the functionality of ARGs. Overall, the review found that there is evidence in the literature that Antimicrobial Resistant (AMR) bacteria are no more heat resistant than non-AMR bacteria. Consequently, recommended heat treatments sufficient to kill non-AMR bacteria in food (70 °C for at least 2 min, or equivalent) should be equally effective in killing AMR bacteria. The literature shows there are several mechanisms through which functional genes from AMR bacteria could theoretically persist in heat-treated food and be transferred to other bacteria. The literature search found sparce published evidence on whether ARGs may actually persist in food after effective heat treatments, and whether functional genes can be transferred to other bacteria. However, three publications have demonstrated that functional ARGs in plasmids may be capable of persisting in foods after effective heat treatments. Given the global impact of AMR, there is clearly a need for further practical research on this topic to provide sufficient evidence to fully assess whether there is a risk to human health from the persistence of functional ARGs in heat-treated and cooked foods.

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Andersson DI, Bampidis V, Bengtsson‐Palme J, Bouchard D, Ferran A, Kouba M, López Puente S, López‐Alonso M, Nielsen SS, Pechová A, Petkova M, Girault S, Broglia A, Guerra B, Innocenti ML, Liébana E, López‐Gálvez G, Manini P, Stella P, Peixe L. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 12: Tetracyclines: tetracycline, chlortetracycline, oxytetracycline, and doxycycline

The specific concentrations of tetracycline, chlortetracycline, oxytetracycline and doxycycline in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. The FARSC for these four tetracyclines was estimated. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for tetracycline, chlortetracycline, oxytetracycline, whilst for doxycycline no suitable data for the assessment were available. Uncertainties and data gaps associated with the levels reported were addressed. It was recommended to perform further studies to supply more diverse and complete data related to the requirements for calculation of the FARSC for these antimicrobials.

Effect of donor-recipient relatedness on the plasmid conjugation frequency: a meta-analysis

BACKGROUND

Conjugation plays a major role in the transmission of plasmids encoding antibiotic resistance genes in both clinical and general settings. The conjugation efficiency is influenced by many biotic and abiotic factors, one of which is the taxonomic relatedness between donor and recipient bacteria. A comprehensive overview of the influence of donor-recipient relatedness on conjugation is still lacking, but such an overview is important to quantitatively assess the risk of plasmid transfer and the effect of interventions which limit the spread of antibiotic resistance, and to obtain parameter values for conjugation in mathematical models. Therefore, we performed a meta-analysis on reported conjugation frequencies from Escherichia coli donors to various recipient species.

RESULTS

Thirty-two studies reporting 313 conjugation frequencies for liquid broth matings and 270 conjugation frequencies for filter matings were included in our meta-analysis. The reported conjugation frequencies varied over 11 orders of magnitude. Decreasing taxonomic relatedness between donor and recipient bacteria, when adjusted for confounding factors, was associated with a lower conjugation frequency in liquid matings. The mean conjugation frequency for bacteria of the same order, the same class, and other classes was 10, 20, and 789 times lower than the mean conjugation frequency within the same species, respectively. This association between relatedness and conjugation frequency was not found for filter matings. The conjugation frequency was furthermore found to be influenced by temperature in both types of mating experiments, and in addition by plasmid incompatibility group in liquid matings, and by recipient origin and mating time in filter matings.

CONCLUSIONS

In our meta-analysis, taxonomic relatedness is limiting conjugation in liquid matings, but not in filter matings, suggesting that taxonomic relatedness is not a limiting factor for conjugation in environments where bacteria are fixed in space.

Detection and linkage to mobile genetic elements of tetracycline resistance gene tet(M) in Escherichia coli isolates from pigs

BACKGROUND

In Escherichia coli the genes involved in the acquisition of tetracycline resistance are mainly tet(A) and tet(B). In addition, tet(M) is the most common tetracycline resistance determinant in enterococci and it is associated with conjugative transposons and plasmids. Although tet(M) has been identified in E. coli, to our knowledge, there are no previous reports studying the linkage of the tet(M) gene in E. coli to different mobile genetic elements. The aim of this study was to determine the occurrence of tet(A), tet(B), and tet(M) genes in doxycycline-resistant E. coli isolates from pigs, as well as the detection of mobile genetic elements linked to tet(M) in E. coli and its possible transfer from enterococci.

RESULTS

tet(A) was the most frequently detected gene (87.9%) in doxycycline-resistant isolates. tet(M) was found in 13.1% E. coli isolates. The tet(M) gene was detected in relation with conjugative transposons in 10 out of 36 enterococci isolates analyzed but not in any of E. coli isolates positive for tet(M). Southern blot showed that in E. coli and in most of the enterococci isolates the tet(M) gene was carried on a plasmid. According to the phylogenetic analysis, E. coli contained a new tet(M) allele grouping separately. Mating experiments revealed that tet(M) was carried on a mobile element successfully transferred between enterococci and between enterococci and E. coli.

CONCLUSIONS

The detection of tet(M) in E. coli isolates from pigs was higher than expected. In our study, tet(M) detected in E. coli seems not to have been transferred from enterococci, although it can not be ruled out that the horizontal transfer of this gene occurred from other intestinal tract bacteria.

Cow excrements enhance the occurrence of tetracycline resistance genes in soil regardless of their oxytetracycline content

Fertilizing soils with animal excrements from farms with common antibiotic use represents a risk of disseminating antibiotic resistance genes into the environment. In the case of tetracycline antibiotics, it is not clear, however, whether the presence of antibiotic residues further enhances the gene occurrence in manured soils. We established a microcosm experiment in which 3 farm soils that had no recent history of fertilization with animal excrements were amended on a weekly basis (9 times) with excrements from either an oxytetracycline-treated or an untreated cow. Throughout the study, the concentration of oxytetracycline in excrements from the treated cow was above 500 μg g(-1)dw, whereas no oxytetracycline was detected in excrements from the healthy cow. Both excrements contained tetracycline resistance (TC-r) genes tet(L), tet(M), tet(V), tet(Z), tet(Q) and tet(W). The excrements from the treated cow also contained the tet(B) gene, and a higher abundance of tet(Z), tet(Q) and tet(W). Three weeks after the last excrement addition, the individual TC-r genes differed in their persistence in soil: tet(Q) and tet(B) were not detectable while tet(L), tet(M), tet(Z) and tet(W) were found in all 3 soils. There were, however, no significant differences in the total number, nor in the abundance, of TC-r genes between soil samples amended with each excrement type. The oxytetracycline-rich and the oxytetracycline-free excrement therefore contributed equally to the increase of tetracycline resistome in soil. Our results indicate that other mechanisms than OTC-selection pressure may be involved in the maintenance of TC-r genes in manured soils.

Cross-sectional study of antimicrobial-resistant bacteria in horses. Part 1: Prevalence of antimicrobial-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus

REASONS FOR PERFORMING STUDY

The increasing prevalence of antimicrobial-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) and antimicrobial-resistant Escherichia coli represents a significant problem. However, the carriage of such bacteria by horses in the UK has not been well characterised.

OBJECTIVES

To estimate the prevalence of nasal carriage of MRSA and faecal carriage of antimicrobial-resistant E. coli amongst horses in the general equine community of the mainland UK.

METHODS

A cross-sectional study of horses recruited by 65 randomly selected equine veterinary practices was conducted, with nasal swabs and faecal samples collected. Faecal samples were cultured for antimicrobial-resistant E. coli. Nasal swabs were cultured for staphylococcal species; methicillin-resistant isolates identified as S. aureus were characterised by SCCmec and spa gene typing. Multilevel logistic regression models were used to calculate prevalence estimates with adjustment for clustering at practice and premises levels. Spatial variation in risk of antimicrobial resistance was also examined.

RESULTS

In total, 650 faecal samples and 678 nasal swabs were collected from 692 horses located on 525 premises. The prevalence of faecal carriage of E. coli with resistance to any antimicrobial was 69.5% (95% CI 65.9-73.1%) and the prevalence of extended-spectrum β-lactamase (ESBL)-producing E. coli was 6.3% (95% CI 4.1-9.6%). The prevalence of nasal carriage of MRSA was 0.6% (95% CI 0.2-1.5%). Spatial analysis indicated variation across the UK for risk of carriage of resistant and multidrug-resistant (resistant to more than 3 antimicrobial classes) E. coli.

CONCLUSIONS AND POTENTIAL RELEVANCE

Carriage of MRSA by horses in the community appears rare, but the prevalence of antimicrobial-resistant E. coli (including ESBL-producing E. coli) is higher. A high prevalence of antimicrobial-resistant bacteria could have significant health implications for the horse population of the UK.

Cross-sectional study of antimicrobial-resistant bacteria in horses. Part 2: Risk factors for faecal carriage of antimicrobial-resistant Escherichia coli in horses

REASONS FOR PERFORMING STUDY

The increasing prevalence of antimicrobial resistant bacteria such as antimicrobial-resistant and extended spectrum β-lactamase (ESBL)-producing Escherichia coli represents a significant problem for human and veterinary medicine. Despite this, the risk factors for faecal carriage of such bacteria by horses in the UK, particularly those in the wider community, have not been well described.

OBJECTIVES

To characterise the risk factors for faecal carriage of antimicrobial-resistant E. coli amongst horses in the mainland UK.

METHODS

A cross-sectional study of horses recruited by 65 randomly selected equine veterinary practices was conducted, with a faecal sample collected and self-administered questionnaire completed by the horse owner. Faecal samples were cultured for antimicrobial-resistant E. coli, with isolates confirmed as E. coli having their antimicrobial resistance profile determined. Multilevel, multivariable logistic regression models were used to investigate risk factors for the carriage of antimicrobial-resistant E. coli in the sample population.

RESULTS

Faecal samples and completed questionnaires were obtained for 627 horses located on 475 premises. Recent hospitalisation, contact with specific types of nonequid animals, the type of premises, the surrounding land use, the reason for veterinary treatment received in the last 6 months and antimicrobial treatment in the previous 10 days were identified as risk factors for many of the antimicrobial-resistance outcomes considered. Being stabled on the same yard as a recently hospitalised horse was identified as a risk factor for increased risk of carriage of ESBL-producing E. coli.

CONCLUSIONS AND POTENTIAL RELEVANCE

Increasing antimicrobial resistance may have significant health implications for the horse population of Great Britain. This form of epidemiological investigation highlights potential risk factors that may be controlled to limit the extent of the problem.

Longitudinal study of antimicrobial-resistant commensal Escherichia coli in the faeces of horses in an equine hospital

The increasing prevalence of antimicrobial resistance in bacteria represents a considerable problem for human and veterinary medicine, causing complications in the treatment of infections. Resistance in Escherichia coli from horses has been documented in commensal and pathogenic strains, but little information exists regarding the prevalence of such bacteria in hospitalised horses or associated risk factors. A longitudinal cohort study was conducted of 103 horses admitted to a referral equine hospital for more than 48 h, with faecal samples collected on hospital admission and subsequently every two days until discharge. Horses undergoing radioactive gamma scintigraphic examination, un-weaned foals and mares with un-weaned foals were excluded. Data were collected from enrolled animals, including antimicrobial treatment history and hospitalisation details. Samples were cultured for resistant E. coli; isolates had their antimicrobial resistance profile determined. High sample prevalence for resistant E. coli was identified for all antimicrobials examined except co-amoxiclav. The prevalence of resistance was consistently lower at admission, rising to a peak 4 days post-admission. Risk factors were analysed using multilevel, multivariable modelling, which identified significant clustering of resistance outcomes within horses. For all outcomes except trimethoprim resistance, the day the sample was obtained was significant, with increased risk of resistance for samples taken on day 2 or later. Antimicrobial treatment in the previous seven days and increased total daily dosages of cotrimoxazole prescribed in the hospital in the previous 24-48 h were associated with increased risk. Location within the hospital and admission reason were significant risk factors for some resistance outcomes. High levels of multidrug-resistant E. coli (47.7% of samples) and extended spectrum β-lactamase-producing E. coli (27.3% of samples) were recovered; such bacteria could significantly complicate treatment if they were the cause of infection and may represent a risk to personnel in close contact with hospitalised horses.

Construction and characterization of Enterococcus faecalis CG110/gfp/pRE25*, a tool for monitoring horizontal gene transfer in complex microbial ecosystems

Enterococci are among the most notorious bacteria involved in the spread of antibiotic resistance (ABR) determinants via horizontal gene transfer, a process that leads to increased prevalence of antibiotic-resistant bacteria. In complex microbial communities with a high background of ABR genes, detection of gene transfer is possible only when the ABR determinant is marked. Therefore, the conjugative multiresistance plasmid pRE25, originating from a sausage-associated Enterococcus faecalis, was tagged with a 34-bp random sequence marker spliced by tet(M). The plasmid constructed, designated pRE25(*) , was introduced into E. faecalis CG110/gfp, a strain containing a gfp gene as chromosomal marker. The plasmid pRE25(*) is fully functional compared with its parental pRE25, occurs at one to two copies per chromosome, and can be transferred to Listeria monocytogenes and Listeria innocua at frequencies of 6 × 10(-6) to 8 × 10(-8) transconjugants per donor. The markers on the chromosome and the plasmid enable independent quantification of donor and plasmid, even if ABR genes occur at high numbers in the background ecosystem. Both markers were stable for at least 200 generations, permitting application of the strain in long-running experiments. Enterococcus faecalis CG110/gfp/pRE25(*) is a potent tool for the investigation of horizontal ABR gene transfer in complex environments such as food matrices, biofilms or colonic models.

Phenotypic and genotypic properties of Escherichia coli isolated from colisepticemic cases of Japanese quail

This study was conducted to characterize the Escherichia coli isolates from colisepticemic Japanese quails. One hundred and nine E. coli were isolated in pure culture from heart blood of dead Japanese quails. The sampled birds were originated from four different farms. Antibiotic resistance pattern of E. coli isolates were determined against nine antibacterial agents. Phylotype and virulence genes of the isolates were detected by polymerase chain reaction. By disc diffusion method, all of the isolates showed resistance to three or more antibiotics, and 19 different patterns of multiple drug resistance were observed. Phylotyping of the most prevalent multiple drug-resistant isolates revealed that they mostly belonged to phylogroups A (A(1) subgroup). The E. coli isolates belong to four phylogenetic groups: A (55.0%), B1 (18.3%), B2 (17.4%), and D (9.2%). Eighty-nine (81.7%) isolates were distributed in five phylogenetic subgroups including 22 (20.2%) in A(0), 38 (34.9%) in A(1), 19 (17.4%) in B2(3), 7 (6.4%) in D(1), and 3 (2.8%) in D(2). The examined E. coli isolates exhibit at least one of the virulence genes tested, whereas three most prevalent genes were crl (94.5%), fimH (89.0%), and iutA (51.4%), respectively. The genetic marker for Afa (afaI B-C), S (sfa/focD-E), and P (papE-F) fimbriae were found in one, four, and ten isolates, respectively. Thirteen different combinations of virulence gene were observed, where combination of crl and fimH genes was the most prevalent pattern. None of the isolates contained the ipaH, stx1, stx2, and eaeA genetic markers. In conclusion, E. coli strains could be considered as a causative agent of mortality in quail farms. In conclusion, E. coli isolates from colisepticemic quails are distributed in different phylogroups, are resistant to combinations of antibiotic agents, and contain several virulence genes.

Natural transfer of sulphonamide and ampicillin resistance between Escherichia coli residing in the human intestine

OBJECTIVES

The aim of this study was to investigate whether the sulphonamide resistance gene sul2 could be transferred between Escherichia coli in the human gut.

METHODS

Nine volunteers ingested a 10(9) cfu suspension of sulphonamide-susceptible, rifampicin-resistant E. coli recipients of human origin. Three hours later, they ingested a 10(7) cfu suspension of a sulphonamide-resistant (MIC>1024 mg/L) E. coli donor of pig origin. Stool samples were collected 24 h prior to ingestion, daily for 7 days and at days 14 and 35. Samples were plated on selective plates and monitored for the acquisition of sulphonamide-resistance by the recipient from the indigenous or administrated donor E. coli. Possible transconjugants were typed by PFGE and tested for the presence of plasmids containing the sul2 gene, which was also sequenced.

RESULTS

Concentrations of the human and animal E. coli reached a maximum of 7.5x10(6) cfu/g faeces and colonized for more than 7 days, and 2x10(8) cfu/g for more than 14 days, respectively. On day 2, a transconjugant was detected in one volunteer. This volunteer was colonized with sulphonamide-resistant E. coli at day 0. The transconjugant was sul2-positive, had an MIC>1024 mg/L for sulfamethoxazole and the same PFGE profile as the recipient. The resident E. coli transferred a plasmid (>63 kb), containing the sul2 gene, to the recipient. The sul2 sequence of the transconjugant was identical to that of the volunteer's own E. coli from day 0, but differed from the animal strain. Co-transfer of ampicillin resistance was also demonstrated.

CONCLUSIONS

Transfer of sul2 was observed between E. coli bacteria in the human intestine. The transconjugant's sul2 gene came from the volunteer's own flora. The origin of the E. coli donor is unknown.

Meta-analysis of experimental data concerning antimicrobial resistance gene transfer rates during conjugation

This paper presents the results of a meta-analysis of published transfer rates of antimicrobial resistance genes. A total of 34 papers were identified, of which 28 contained rates estimated in relation to either donor or recipient bacterial counts. The published rates ranged from 10(-2) to 10(-9). Generalized linear modeling was conducted to identify the factors influencing this variation. Highly significant associations between transfer frequency and both the donor (P = 1.2 x 10(-4)) and recipient (P = 1.0 x 10(-5)) genera were found. Also significant was whether the donor and recipient strains were of the same genus (P = 0.023) and the nature of the genetic element (P = 0.0019). The type of experiment, in vivo or in vitro, approached statistical significance (P = 0.12). Parameter estimates from a general linear model were used to estimate the probability of transfer of antimicrobial resistance genes to potential pathogens in the intestine following oral ingestion. The mean logarithms of these probabilities are in the range of [-7.0, -3.1]. These probability distributions are suitable for use in the quantitative assessment of the risk of transfer of antimicrobial resistance genes to the intestinal flora of humans and animals.