Marine integrons containing novel integrase genes,attachment sites,attI, and associated gene cassettes in polluted sediments from Suez and Tokyo Bays

In order to understand the structure and biological significance of integrons and associated gene cassettes in marine polluted sediments, metagenomic DNAs were extracted from sites at Suez and Tokyo Bays. PCR amplicons containing new integrase genes, intI, linked with novel gene cassettes, were recovered and had sizes from 1.8 to 2.5 kb. This approach uncovered, for the first time, the structure and diversity of both marine integron attachment site, attI, and the first gene cassette, the most efficiently expressed integron-associated gene cassette. The recovered 13 and 20 intI phylotypes, from Suez and Tokyo Bay samples, respectively, showed a highly divergence, suggesting a difference in integron composition between the sampling sites. Some intI phylotypes showed similarity with that from Geobacter metallireducens, belonging to Deltaproteobacteria, the dominant class in both sampling sites, as determined by 16S rRNA gene analysis. Thirty distinct families of putative attI site, as determined by the presence of an attI-like simple site, were recovered. A total of 146 and 68 gene cassettes represented Suez and Tokyo Bay unsaturated cassette pools, respectively. Gene cassettes, including a first cassette, from both sampling sites encoded two novel families of glyoxalase/bleomycin antibiotic-resistance protein. Gene cassettes from Suez Bay encoded proteins similar to haloacid dehalogenases, protein disulfide isomerases and death-on-curing and plasmid maintenance system killer proteins. First gene cassettes from Tokyo Bay encoded a xenobiotic-degrading protein, cardiolipin synthetase, esterase and WD40-like β propeller protein. Many of the first gene cassettes encoded proteins with no ascribable function but some of them were duplicated and possessed signal functional sites, suggesting efficient adaptive functions to their bacterial sources. Thus, each sampling site had a specific profile of integrons and cassette types consistent with the hypothesis that the environment shapes the genome.     

Distribution and characterization of integrons in Escherichia coli strains of animal and human origin

One hundred and twenty clinical and commensal Escherichia coli strains isolated in Switzerland from humans and from companion and farm animals were analysed for the prevalence of integrons of classes 1, 2, and 3 and for the characterization of their gene cassettes. The relationships between integron carriage and host category, and between integron carriage and phylogenetic E. coli lineage were also analysed. Integrons were detected in 48 (40%) of the isolates and were thus widely disseminated in the human and animal E. coli strains considered. Moreover, the association between integron carriage and certain animal categories (farm animals) suggests that animals that are raised for economic purposes might be exposed to a major antibiotic pressure. Finally, our data confirm that E. coli commensal strains represent a significant source of antibiotic-resistant determinants.     

Characterization of antimicrobial resistant Escherichia coli isolated from processed bison carcasses

AIM: To determine the phenotypic and genotypic antimicrobial susceptibility profiles of Escherichia coli from bison carcasses. METHODS AND MATERIALS: The antimicrobial resistance of 138 E. coli isolates recovered from processed bison carcasses was determined by using the National Antimicrobial Resistance Monitoring System panels, polymerase chain reaction assays, plasmid analysis and conjugation studies. RESULTS: Resistance to 14 of the 16 antimicrobials was observed. Twenty-three (16.7%) isolates displayed resistance to at least one antimicrobial agent. The most prevalent resistances were to tetracycline (13.0%), sulfamethoxazole (7.9%) and streptomycin (5.8%). No resistance was observed to amikacin and ciprofloxacin. Further analysis of 23 antimicrobial-resistant E. coli isolates showed the presence of resistance genes corresponding to their phenotypic profiles. Results of conjugation studies carried out showed most isolates tested were able to transfer their resistance to recipients. CONCLUSION: This study indicated that multidrug-resistant E. coli isolates are present in bison. However, the resistance rate is lower than that reported in other meat species. SIGNIFICANCE AND IMPACT OF THE STUDY: The beneficial effects of antimicrobial-free feeding practice in bison may be promoting a reduction in the prevalence of antimicrobial resistance in commensal flora of bison.     

Recoding of synonymous genes to expand evolutionary landscapes requires control of secondary structure affecting translation

Synthetic DNA design needs to harness the many information layers embedded in a DNA string. We previously developed the Evolutionary Landscape Painter (ELP), an algorithm that exploits the degeneracy of the code to increase protein evolvability. Here, we have used ELP to recode the integron integrase gene (intI1) in two alternative alleles. Although synonymous, both alleles yielded less IntI1 protein and were less active in recombination assays than intI1. We spliced the three alleles and mapped the activity decrease to the beginning of alternative sequences. Mfold predicted the presence of more stable secondary structures in the alternative genes. Using synonymous mutations, we decreased their stability and recovered full activity. Following a design‐build‐test approach, we have now updated ELP to consider such structures and provide streamlined alternative sequences. Our results support the possibility of modulating gene activity through the ad hoc design of 5′ secondary structures in synthetic genes.     

High occurrence of carbapenem-resistant Escherichia coli isolates from healthy rabbits (Oryctolagus cuniculus): first report of blaIMI and blaVIM type genes from livestock in Tunisia

We aimed to study the antibiotic susceptibility and possible occurrence of extended-spectrum beta-lactamases (ESBL)/carbapenemase-producing Escherichia coli isolates collected from rabbits in Tunisia. In all, 35 faecal samples from healthy rabbits were collected from one farm and E. coli were isolated from three media: antibiotic-free TBX agar, TBX+2 mg l⁻¹ cefotaxime and TBX+1 mg l⁻¹ imipenem. In total, 39 E. coli isolates were recovered; the majority showed resistance to at least one antibiotic and none was ESBL producer. Carbapenem resistance was detected in 16 isolates from either selective or un-selective media. Phenotypic methods used to detect carbapenemase production showed two positive isolates by Modified Hodge Test, six metallo-carbapenemase producers (Imipenem disc+EDTA) and all were temocillin resistant (possible OXA-48 carbapenemase). bla_VIM and bla_IMP type genes were detected in two and one isolates, respectively; one of them harboured both genes. Isolates contained common genes encoding resistance to sulphonamides (sul1, sul2), tetracycline (tetA, tetB, tetC) and fluoroquinolones (qnrS, aac(6′)-Ib-cr). Class 1 and 2 integrons were detected in five and four isolates, respectively. These findings highlight the importance of rabbit production as reservoir of carbapenem-resistant E. coli and argument the first report of bla_VIM and bla_IMP genes in livestock in Tunisia.     

Analysis of integrons in clinical isolates of Escherichia coli in China during the last six years

A multiple PCR for the detection of the integrase genes of the three classes of integrons was carried out, and their gene cassettes were characterized in 111 clinical strains of Escherichia coli isolated in Guangzhou City, China during the last 6 years. IntI1 and intI2 genes were detected in 95 isolates (85.6%) and four isolates (3.6%), respectively. No intI3 gene was detected. Six different gene cassettes were found in these strains, and a high prevalence of dfr and aad genes was observed. The E. coli isolates that contained a 1664-bp amplicon of dfrA17-aadA5 in class 1 integron were found to be phylogenetically unrelated to each other by using the enterobacterial repetitive intergenic consensus PCR, as the cassette could be transferred to recipient strains, indicating that the gene cassettes might be disseminated in the clinical strains by a horizontal gene transfer. Therefore, it is important that guidelines for the prudent use of antimicrobial agents are adopted and surveillance programs are established.     

Survey of Shiga toxigenic Escherichia coli O157 and drug-resistant coliform bacteria from in-line milk filters on dairy farms in the Czech Republic

Aims: To determine the occurrence of Shiga toxin‐producing Escherichia coli (STEC) O157 and coliform bacteria isolates resistant to antimicrobial agents in dairy herds by examining milk filters and to analyse the influence of management factors and antibiotic use on antimicrobial resistance. Methods and Results: A total of 192 in‐line milk filters were sampled on 192 dairy farms in the Czech Republic. Information on feeding, husbandry, production, and antibiotic therapy were obtained by questionnaire. The milk filters were cultured for STEC O157 and coliform bacteria. All recovered isolates were examined for antimicrobial susceptibility and presence of antimicrobial‐resistance genes. STEC O157 was detected in four (2%) of the filters. Resistant nonpathogenic E. coli and coliform bacteria isolates with specific genes were detected in 44 (23%) of the filters. Conclusions: The study demonstrated a high prevalence of resistant coliform bacteria in milk filters obtained on Czech dairy farms. Significance and Impact of the Study: The occurrence of resistant coliform bacteria in milk filters was significantly higher among isolates from farms where antibiotic therapy against mastitis was employed during the dry period (P < 0·05).     

High prevalence of antimicrobial-resistant genes and integrons in Escherichia coli isolates from Black-headed Gulls in the Czech Republic

AIMS: To carry out an assessment of the occurrence of resistance to antimicrobials in Escherichia coli that has been isolated from young Black-headed Gulls in three nesting colonies. METHODS AND RESULTS: A total of 257 isolates were tested for sensitivity to eight antibacterial substances by disk diffusion method. The polymerase chain reaction was used for detecting specific genes of antibacterial resistance and class 1 integrons in resistant E. coli isolates. A total 75 (29.9%) of 257 isolates were resistant to one or more antimicrobial agents. The dominant type of resistance was to tetracycline, detected in 49 (19.1%) isolates. Resistance to ampicillin was detected in 30 (11.7%), cephalothin in 11 (4.3%), streptomycin in 24 (9.3%), sulphonamides in 20 (7.8%) and chloramphenicol in 5 (1.9%) isolates. Nine isolates carrying integrons were detected. CONCLUSIONS: The study suggests that young Black-headed Gulls are an important host reservoir of resistant E. coli strains, probably reflecting the presence of such strains in their sources of food and/or water. SIGNIFICANCE AND IMPACT OF THE STUDY: Although Black-headed Gulls do not naturally come into contact with antibiotics, these birds can be infected with resistant E. coli and potentially serve as their reservoirs, vectors and bioindicators in the environment.     

临床产ESBLs大肠埃希菌整合子检测及基因型分析

了解临床分离的产ESBLs大肠埃希菌(ESBLs-producing Escherichia coli,ESBL-EC)中Ⅰ、Ⅱ、Ⅲ类整合子及ESBL-EC基因型的分布。收集2014年1月至12月某三甲医院住院患者分离的大肠埃希菌,经全自动细菌分析系统鉴定并检测其对临床常用抗菌药物的耐药性,双纸片协同试验确定ESBL-EC,采用聚合酶链反应(PCR)对整合子基因和ESBLs基因进行检测。K-B法比较整合子阳性菌株与阴性菌株的耐药率。结果发现,98株临床非重复ESBL-EC对青霉素类、头孢菌素类、喹诺酮类、单环酰胺类和庆大霉素耐药率均大于50%,对妥布霉素耐药率为31.62%,对呋喃妥因、阿莫西林/克拉维酸和阿米卡星较敏感,分别为11.11%、13.4%和6.12%;对碳青霉烯类抗菌素、替加环素和哌拉西林/他唑巴坦敏感率为100%。98株菌中检出47株含Ⅰ类整合子(47.96%),3株含Ⅱ类整合子(3.06%),所有菌株中有1株同时含Ⅰ类和Ⅱ类整合子,未检出Ⅲ类整合子。整合子阳性菌株对四环素和复方新诺明的耐药率高于整合子阴性菌株(P0.05)。98株菌中β-内酰胺酶基因TEM、CTX-M-9、CTX-M-1、CTX-M-2和SHV阳性率分别为62.24%、53.06%、32.65%、4.08%和3.06%,ESBL-EC基因分型分布以TEM合并CTX-M-9型(共30株)最多见,占30.61%。结果表明,Ⅰ类整合子在产ESBLs大肠埃希菌中分布广泛,本研究尚不足以证明整合子的存在可影响ESBL-EC菌株抗生素耐药水平。同时携带TEM和CTX-M-9基因是安徽医科大学解放军174临床学院产ESBLs大肠埃希菌临床耐药菌株产生的主要原因。