Class 1 integrons and their conjugal transfer with and without virulence-associated genes in extra-intestinal and intestinal Escherichia coli of poultry

High incidence of multidrug resistance and class 1 and 2 integrons in Escherichia coli isolated from broiler chickens in South of Iran

The objective was to investigate the multidrug resistance and presence of class 1 and 2 integrons in 300 Escherichia coli isolates obtained from 20 broiler farms during three rearing periods (one-day-old chicks, thirty-day-old chickens, and one day before slaughter) in Fars, South Iran. Results showed that 81.00%, 82.00%, and 85.00% of isolates were multidrug-resistant on the first day, thirty-day-old chickens, and one day before slaughter, respectively. Multidrug-resistant E. coli isolates were further examined for the presence of class 1 and 2 integrons using PCR assay. The existence of class 1 integron-integrase gene (intI1) was confirmed in 68.40%, 72.70%, and 60.90% of multidrug-resistant isolates from stage 1, stage 2, and stage 3 of the rearing period, respectively. The frequency of class 2 integron-integrase gene (intI2) during the first to the third stage of sampling was 2.60%, 25.50%, and 30.40%. Also, sequence analysis of the cassette arrays within class 1 integron revealed the presence of the genes associated with resistance for trimethoprim (dfrA), streptomycin (aadA), erythromycin (ereA), and orfF genes. The results revealed that percentages of antimicrobial resistance in E. coli isolates were significantly higher in the middle and end stages of the rearing period. In conclusion, widespread dissemination of class 1 integrons in all three stages and rising trends of class 2 integrons existence in E. coli isolates during the rearing period of broiler chickens could exacerbate the spread of resistance factors among bacteria in the poultry industry. Future research is needed to clarify its implication for human health.

Occurrence and molecular characteristics of antimicrobial resistance of Escherichia coli from broilers, pigs and meat products in Thailand and Cambodia provinces

Nine hundred and forty-one samples were collected in Sa Keao, Thailand (n = 554) and Banteay Meanchey, Cambodia (n = 387) from July 2014 to January 2015. A total of 667 Escherichia coli isolates (381 isolates from Sa Keao and 286 isolates from Banteay Meanchey) were obtained and examined for antimicrobial susceptibility, class 1 integrons, ESBL genes and horizontal transfer of resistance determinants. Prevalence of E. coli in pig and broiler carcass samples from slaughterhouses and fresh markets was 36-85% in Sa Keao and 11-69% in Banteay Meanchey. The majority of these isolates were multidrug resistant (75.3%). Class 1 integrons were common in both Thai (47%) and Cambodian (62%) isolates, of which four resistance gene cassette arrays including aadA1, dfrA1-aadA1, dfrA12-aadA2 and aadA2-linF were identified. Class 1 integrons in two broiler isolates from Sa Keao (dfrA12-aadA2) and one broiler isolate from Banteay Meanchey (dfrA1-aadA1) were horizontally transferable. Sixteen isolates were confirmed to be ESBL-producing strains with ESBL gene blaCTX-M-15 , broad spectrum β-lactamase gene blaTEM-1 and the AmpC gene blaCMY-2 being detected. The blaTEM-1 gene was most prevalent and located on a conjugative plasmid.

Integrons: Vehicles and pathways for horizontal dissemination in bacteria

Integrons are genetic elements first described at the end of the 1980s. Although most integrons were initially described in human clinical isolates, they have now been identified in many non-clinical environments, such as water and soil. Integrons are present in ≈10% of the sequenced bacterial genomes and are frequently linked to mobile genetic elements (MGEs); particularly the class 1 integrons. Genetic linkage to a diverse set of MGEs facilitates horizontal transfer of class 1 integrons within and between bacterial populations and species. The mechanistic aspects limiting transfer of MGEs will therefore limit the transfer of class 1 integrons. However, horizontal movement due to genes provided in trans and homologous recombination can result in class 1 integron dynamics independent of MGEs. A key determinant for continued dissemination of class 1 integrons is the probability that transferred MGEs will be vertically inherited in the recipient bacterial population. Heritability depends both on genetic stability as well as the fitness costs conferred to the host. Here we review the factors known to govern the dissemination of class 1 integrons in bacteria.

Multidrug resistant commensal Escherichia coli in animals and its impact for public health

After the era of plentiful antibiotics we are alarmed by the increasing number of antibiotic resistant strains. The genetic flexibility and adaptability of Escherichia coli to constantly changing environments allows to acquire a great number of antimicrobial resistance mechanisms. Commensal strains of E. coli as versatile residents of the lower intestine are also repeatedly challenged by antimicrobial pressures during the lifetime of their host. As a consequence, commensal strains acquire the respective resistance genes, and/or develop resistant mutants in order to survive and maintain microbial homeostasis in the lower intestinal tract. Thus, commensal E. coli strains are regarded as indicators of antimicrobial load on their hosts. This chapter provides a short historic background of the appearance and presumed origin and transfer of antimicrobial resistance genes in commensal intestinal E. coli of animals with comparative information on their pathogenic counterparts. The dynamics, development, and ways of evolution of resistance in the E. coli populations differ according to hosts, resistance mechanisms, and antimicrobial classes used. The most frequent tools of E. coli against a variety of antimicrobials are the efflux pumps and mobile resistance mechanisms carried by plasmids and/or other transferable elements. The emergence of hybrid plasmids (both resistance and virulence) among E. coli is of further concern. Co-existence and co-transfer of these "bad genes" in this huge and most versatile in vivo compartment may represent an increased public health risk in the future. Significance of multidrug resistant (MDR) commensal E. coli seem to be highest in the food animal industry, acting as reservoir for intra- and interspecific exchange and a source for spread of MDR determinants through contaminated food to humans. Thus, public health potential of MDR commensal E. coli of food animals can be a concern and needs monitoring and more molecular analysis in the future.

Antimicrobial resistance and genetic characteristics of integron-carrier shigellae isolated in Hungary (1998-2008)

Antimicrobial susceptibility, integron carriage, genetic relationship and presence of some important virulence genes of the integron-carrier strains of Shigella sonnei (n = 230) and Shigella flexneri (n = 22) isolated from stool samples of patients in Hungary between 1998 and 2008 were investigated. Sixty-seven per cent (168/252) of the strains were resistant to sulfamethoxazole/trimethoprim (SxT) followed by streptomycin (S, 47%), ampicillin (A, 32%) and tetracycline (Tc, 28%). Thirty-six per cent (90/252) exhibited multidrug resistance, mostly showing SSxTTc or ASSxTc, ASSxTTc resistance patterns. An S. sonnei strain of imported origin was resistant to cefotaxime and harboured a blaCTX-M-55-type extended-spectrum β-lactamase gene. Altogether 33% of the S. sonnei (n = 75) and 14% of the S. flexneri (n = 3) strains had either class 1 or class 2 integrons or both. The variable regions encoded aadA1 or dfrA1-aadA1 genes for the class 1 and dfrA1-sat2-aadA1 or dfrA1-sat2 genes for the class 2 integrons. Pulsed-field gel electrophoresis analysis revealed that those strains that have different integron types represented different genetic clusters. The Shiga toxin (stx1) gene was identified in one S. sonnei strain and the cdtB gene was detected in an S. flexneri strain. The results reveal the high incidence of antibiotic resistance among Shigella isolates and the presence of the stx1 gene in S. sonnei and the cdtB gene in S. flexneri. The genetic diversity of Shigella spp. isolated recently in Hungary was also demonstrated.

Genetic and phylogenetic analysis of avian extraintestinal and intestinal Escherichia coli

Extraintestinal pathogenic Escherichia coli (ExPEC) isolates of animals and man are known to carry specific virulence associated genes. The intestinal tract, it is primarily colonized by various strains of commensal E. coli but it may include ExPEC as well. Here we aimed to assess possible genetic and evolutionary linkages between extraintestinal pathogenic and intestinal (commensal) E. coli of poultry. For that purpose we analysed 71 ExPEC isolates, and 40 intestinal isolates assumed to be commensal E. coli (IntEC), from dead chickens and turkey poults for 26 virulence related genes. Although the two groups shared several virulence determinants the genes pic, papC, and cdtIV were exclusively present in ExPEC and further five genes (colV, iss, kpsM, tsh and iutA), were significantly more frequent among ExPEC. Phylogenetic backgrounds of ExPEC and of IntEC isolates indicated significant differences. A 40% of ExPEC belonged to phylogroup A primarily containing strains of serogroup O78. Phylogroup D contained ExPEC strains of serogroups O53 (2 strains) and O115 (5 strains) characterized by the cdt-IV genes, suggesting the existence of new clones of avian ExPEC in phylogenetic group D. On the other hand, a 42.5% of IntEC belonged to phylogroup B1 with diverse serogroups. Our data provide insight into the clonal evolution of avian ExPEC especially in phylogenetic groups A and D, resulting avian ExPEC with similarities to human ExPEC.

Impact of feed supplementation with antimicrobial agents on growth performance of broiler chickens, Clostridium perfringens and enterococcus counts, and antibiotic resistance phenotypes and distribution of antimicrobial resistance determinants in Escherichia coli isolates

The effects of feed supplementation with the approved antimicrobial agents bambermycin, penicillin, salinomycin, and bacitracin or a combination of salinomycin plus bacitracin were evaluated for the incidence and distribution of antibiotic resistance in 197 commensal Escherichia coli isolates from broiler chickens over 35 days. All isolates showed some degree of multiple antibiotic resistance. Resistance to tetracycline (68.5%), amoxicillin (61.4%), ceftiofur (51.3%), spectinomycin (47.2%), and sulfonamides (42%) was most frequent. The levels of resistance to streptomycin, chloramphenicol, and gentamicin were 33.5, 35.5, and 25.3%, respectively. The overall resistance levels decreased from day 7 to day 35 (P < 0.001). Comparing treatments, the levels of resistance to ceftiofur, spectinomycin, and gentamicin (except for resistance to bacitracin treatment) were significantly higher in isolates from chickens receiving feed supplemented with salinomycin than from the other feeds (P < 0.001). Using a DNA microarray analysis capable of detecting commonly found antimicrobial resistance genes, we characterized 104 tetracycline-resistant E. coli isolates from 7- to 28-day-old chickens fed different growth promoters. Results showed a decrease in the incidence of isolates harboring tet(B), bla(TEM), sulI, and aadA and class 1 integron from days 7 to 35 (P < 0.01). Of the 84 tetracycline-ceftiofur-resistant E. coli isolates, 76 (90.5%) were positive for bla(CMY-2). The proportions of isolates positive for sulI, aadA, and integron class 1 were significantly higher in salinomycin-treated chickens than in the control or other treatment groups (P < 0.05). These data demonstrate that multiantibiotic-resistant E. coli isolates can be found in broiler chickens regardless of the antimicrobial growth promoters used. However, the phenotype and the distribution of resistance determinants in E. coli can be modulated by feed supplementation with some of the antimicrobial agents used in broiler chicken production.

Chronological study of antibiotic resistances and their relevant genes in Korean avian pathogenic Escherichia coli isolates

Antibiograms and relevant genotypes of Korean avian pathogenic Escherichia coli (APEC) isolates (n = 101) recovered between 1985 and 2005 were assessed via disc diffusion test, PCR, restriction enzyme analysis, and sequencing. These isolates were highly resistant to tetracycline (84.2%), streptomycin (84.2%), enrofloxacin (71.3%), and ampicillin (67.3%), and most of the tetracycline, streptomycin, enrofloxacin, and ampicillin resistances were associated with tetA and/or tetB, aadA and/or strA-strB, mutations in gyrA and/or parC, and TEM, respectively. Class 1 integrons were detected in 40 isolates (39.6%), and a variety of gene cassettes conferring streptomycin (aadA), gentamicin (aadB), and trimethoprim (dfr) resistances were identified: aadA1a (27.5%), dfrV-orfD (2.5%), aadB-aadA1a (2.5%), dfrI-aadA1a (47.5%), dfrXVII-aadA5 (12.5%), and dfrXII-orfF-aadA2 (7.5%). In addition, several types of common promoters (P(ant)) of the gene cassettes (hybrid P1, weak P1, or weak P1 plus P2) and single-nucleotide polymorphisms in aadA1a were identified. The results of a chronological analysis demonstrated significant and continuous increases in the frequencies of resistances to several antibiotics (tetracycline, streptomycin, enrofloxacin, ampicillin, and trimethoprim-sulfamethoxazole) and of the relevant resistance genes (tetA, strA-strB, and TEM), mutations in gyrA and parC, and multidrug-resistant APEC strains during the period 2000 to 2005.

Antibiotic resistance and virulence genes in commensal Escherichia coli and Salmonella isolates from commercial broiler chicken farms

Antibiotic resistance patterns and the presence of antibiotic and virulence determinants in 74 sorbitol-negative Escherichia coli and 62 Salmonella isolates from nine different broiler chicken farms were investigated. Each farm was supplied by one of three companies that used different antimicrobial agents in feed for growth promotion. The isolates were identified by API 20E for E. coli and by serological tests for Salmonella. The susceptibility of the isolates to antibiotics was determined by Sensititre using the Clinical and Laboratory Standards Institute's breakpoints. Fifty-two E. coli isolates (70.3%) and nine Salmonella isolates (14.52%) were multiresistant to at least nine antibiotics. The multiresistant isolates were evaluated for the presence of tetracycline resistance, integron class 1, and blacMY 2 genes by PCR. Of the 74 E. coli isolates, 55 were resistant to amoxicillin and ceftiofur. Among these 55 resistant E. coli isolates, 45 (81.8%) and 22 (40.0%) were positive for blacMY-2 and qacEdeltal-Sull genes, respectively. Tetracycline resistance was found in 56 isolates (75.8%) among which 12 (21.4%) and 24 (42.9%) gave positive results for tetA and tetB, respectively. Virulence genes (iss, tsh, and traT), aerobactin operon (iucC), and the eaeA gene were detected in some E. coli strains. Among the 27 amoxicillin- and ceftiofur-resistant Salmonella isolates, the blacMY-2 gene was detected in 22 isolates. The class 1 integron gene (qacEdeltal-Sull) was not detected in any Salmonella isolates, whereas the invasin (inv) and virulence (spy) genes were found in 61 (98.4%) and 26 (42%) of the Salmonella isolates, respectively. This study indicated that multiple antibiotic-resistant commensal E. coli and Salmonella strains carrying virulence genes can be found on commercial broiler chicken farms and may provide a reservoir for these genes in chicken production facilities. Except for the presence of tetB, there was no significant effect of feed formulations on the phenotypic or genotypic characteristics of the isolates.