Fast, economic and simultaneous identification of clinically relevant Gram-negative species with multiplex real-time PCR

Aim: A newly designed multiplex real-time PCR (rt-PCR) was validated to detect four clinically relevant Gram-negative bacteria (Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae and Pseudomonas aeruginosa). Materials & methods: Serial dilutions of genomic DNA were used to determine the limit of detection. Colony PCR was performed with isolates of the four selected species and other species as negative controls. Isolates were characterized genotypically and phenotypically to evaluate the assay. Results: Specific signals of all target genes were detected with diluted templates comprising ten genomic equivalents. Using colony rt-PCR, all isolates of the target species were identified correctly. All negative control isolates were negative. Conclusion: The genes gad, basC, khe and ecfX can reliably identify these four species via multiplex colony rt-PCR. © 2018 Daniel Weiss

Occurrence, Phenotypic and Molecular Characteristics of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in Healthy Turkeys in Northern Egypt

Poultry is one of the most important reservoirs for zoonotic multidrug-resistant pathogens. The indiscriminate use of antimicrobials in poultry production is a leading factor for development and dissemination of antimicrobial resistance. This study aimed to describe the prevalence and antimicrobial resistance of E. coli isolated from healthy turkey flocks of different ages in Nile delta region, Egypt. In the current investigation, 250 cloacal swabs were collected from 12 turkey farms in five governorates in the northern Egypt. Collected samples were cultivated on BrillianceTM ESBL agar media supplemented with cefotaxime (100 mg/L). The E. coli isolates were identified using MALDI-TOF-MS and confirmed by a conventional PCR assay targeting 16S rRNA-DNA. The phenotypic antibiogram against 14 antimicrobial agents was determined using the broth micro-dilution method. DNA-microarray-based assay was applied for genotyping and determination of both, virulence and resistance-associated gene markers. Multiplex real-time PCR was additionally applied for all isolates for detection of the actual most relevant Carbapenemase genes. The phenotypic identification of colistin resistance was carried out using E-test. A total of 26 E. coli isolates were recovered from the cloacal samples. All isolates were defined as multidrug-resistant. Interestingly, two different E. coli strains were isolated from one sample. Both strains had different phenotypic and genotypic profiles. All isolates were phenotypically susceptible to imipenem, while resistant to penicillin, rifampicin, streptomycin, and erythromycin. None of the examined carbapenem resistance genes was detected among isolates. At least one beta-lactamase gene was identified in most of isolates, where blaTEM was the most commonly identified determinant (80.8%), in addition to blaCTX-M9 (23.1%), blaSHV (19.2%) and blaOXA-10 (15.4%). Genes associated with chloramphenicol resistance were floR (65.4%) and cmlA1 (46.2%). Tetracycline- and quinolone-resistance-associated genes tetA and qnrS were detected in (57.7%) and (50.0%) of isolates, respectively. The aminoglycoside resistance associated genes aadA1 (65.4%), aadA2 (53.8%), aphA (50.0%), strA (69.2%), and strB (65.4%), were detected among isolates. Macrolide resistance associated genes mph and mrx were also detected in (53.8%) and (34.6%). Moreover, colistin resistance associated gene mcr-9 was identified in one isolate (3.8%). The class 1 integron integrase intI1 (84.6%), transposase for the transposon tnpISEcp1 (34.6%) and OqxB -integral membrane and component of RND-type multidrug efflux pump oqxB (7.7%) were identified among the isolates. The existing high incidence of ESBL/colistin-producing E. coli identified in healthy turkeys is a major concern that demands prompt control; otherwise, such strains and their resistance determinants could be transmitted to other bacteria and, eventually, to people via the food chain

Characterisation of S. aureus/MRSA CC1153 and review of mobile genetic elements carrying the fusidic acid resistance gene fusC

While many data on molecular epidemiology of MRSA are available for North America, Western Europe and Australia, much less is known on the distribution of MRSA clones elsewhere. Here, we describe a poorly known lineage from the Middle East, CC1153, to which several strains from humans and livestock belong. Isolates were characterised using DNA microarrays and one isolate from the United Arab Emirates was sequenced using Nanopore technology. CC1153 carries agr II and capsule type 5 genes. Enterotoxin genes are rarely present, but PVL is common. Associated spa types include t504, t903 and t13507. PVL-positive CC1153-MSSA were found in Egyptian cattle suffering from mastitis. It was also identified among humans with skin and soft tissue infections in Saudi Arabia, France and Germany. CC1153-MRSA were mainly observed in Arabian Gulf countries. Some isolates presented with a previously unknown SCCmec/SCCfus chimeric element in which a mec B complex was found together with the fusidic acid resistance gene fusC and accompanying genes including ccrA/B-1 recombinase genes. Other isolates carried SCCmec V elements that usually also included fusC. Distribution and emergence of CC1153-MRSA show the necessity of molecular characterization of MRSA that are resistant to fusidic acid. These strains pose a public health threat as they combine resistance to beta-lactams used in hospitals as well as to fusidic acid used in the community. Because of the high prevalence of fusC-positive MRSA in the Middle East, sequences and descriptions of SCC elements harbouring fusC and/or mecA are reviewed. When comparing fusC and its surrounding regions from the CC1153 strain to available published sequences, it became obvious that there are four fusC alleles and five distinct types of fusC gene complexes reminiscent to the mec complexes in SCCmec elements. Likewise, they are associated with different sets of ccrA/B recombinase genes and additional payload that might include entire mec complexes or SCCmec elements

EARLINET instrument intercomparison campaigns: Overview on strategy and results

This paper introduces the recent European Aerosol Research Lidar Network (EARLINET) quality-assurance efforts at instrument level. Within two dedicated campaigns and five single-site intercomparison activities, 21 EARLINET systems from 18 EARLINET stations were intercompared between 2009 and 2013. A comprehensive strategy for campaign setup and data evaluation has been established. Eleven systems from nine EARLINET stations participated in the EARLINET Lidar Intercomparison 2009 (EARLI09). In this campaign, three reference systems were qualified which served as traveling standards thereafter. EARLINET systems from nine other stations have been compared against these reference systems since 2009. We present and discuss comparisons at signal and at product level from all campaigns for more than 100 individual measurement channels at the wavelengths of 355, 387, 532, and 607 nm. It is shown that in most cases, a very good agreement of the compared systems with the respective reference is obtained. Mean signal deviations in predefined height ranges are typically below ±2 %. Particle backscatter and extinction coefficients agree within ±2  ×  10−4 km−1 sr−1 and ± 0.01 km−1, respectively, in most cases. For systems or channels that showed larger discrepancies, an in-depth analysis of deficiencies was performed and technical solutions and upgrades were proposed and realized. The intercomparisons have reinforced confidence in the EARLINET data quality and allowed us to draw conclusions on necessary system improvements for some instruments and to identify major challenges that need to be tackled in the future

The geographies of ancient Ephesus and the Artemision in Anatolia

WOS: 000243163500007This study is a sedimentologic and geomorphologic analysis of ancient geographies of the floodplains and delta of the Kucuk Menderes (ancient Cayster River) around the city of Ephesus and the Artemision in Aegean coastal Anatolia. The authors emphasize the interrelationship of archaeological dating and structure, and historical comment in interdisciplinary analysis of ancient geographies and their paleoenvironments. In some cases, the historical literature is specific and factual. In other cases, legend from prehistory may provide important clues to the reconstruction of ancient environments as related to archaeological and historical settings. Ephesus and the closely related Artemision, or Temple of Diana of the Ephesians, offer a chance to link the disciplines of geology, physical geography, archaeology, history, and epigraphy in a composite of paleoenvironmental/paleogeographical interpretations of geomorphology over the past three millennia. Holocene sea-level rise and marine transgression provide the raised paralic settings of the harbors of Ephesus and the Artemision. The settings of the harbors were altered by continuing progradation of the ancient Cayster River delta-floodplain over the past three millennia. This research shows how interdisciplinary research greatly enhances our understanding of the ancient geographies of Ephesus and the Artemision. (c) 2007 Wiley Periodicals, Inc