Sequence analysis of rpoB mutations in rifampin-resistant clinical Mycobacterium tuberculosis isolates from Turkey

Drug-resistant tuberculosis is a serious problem throughout the world. Resistance to Rifampicin (RIF) is mainly caused by the mutations in the rpoB gene coding the beta-subunit of RNA polymerase. In this study, we aimed to detect the distribution of rpoB gene mutations in 80 RIF-resistant clinical Mycobacterium tuberculosis (MTB) isolates from Turkey. The rpoB gene was amplified by PCR and mutations leading to RIF resistance were determined by automated sequence analysis. A total of 72 of the 80 isolates (90%) were found to carry mutations in the amplified region, whereas eight isolates (10%) carried no mutations. Overall, 24 different missense mutations affecting 14 codons, and two deletion mutants were identified. Nine new mutations, six in the hot-spot region and three outside this region, were found. The codon numbers of the most frequently encountered mutations were 531 (51.4%), 526 (18.1%), 516 (13.9%), and 513 (12.5%). As a result, 90% of the RIF-resistant MTB isolates from the Turkish patients were found to carry a mutation in the rpoB gene, Ser531Leu being the most frequent one. Although molecular methods identify mutations leading to RIF resistance very quickly, results of the antimycobacterial susceptibility tests must be taken into consideration for the patients carrying no mutations in this region

Fecal Carriage of Extended‑spectrum Beta‑lactamase and AmpC Beta‑lactamase‑producing Enterobacteriaceae in a Turkish Community

Background: Community‑acquired infection caused by extended‑spectrum beta‑lactamase (ESBL)‑producing microorganisms has an increasing frequency. Aim: The aim of this study was to determine the fecal carriage of ESBL and AmpC beta‑lactamase‑producing Enterobacteriaceae in community and to investigate cefotaxime‑M (CTX‑M) genes among ESBL isolates. Materials and Methods: A total of 1402 fecal specimens which were collected from outpatients included in the study. ESBL screening, ESBL production, and AmpC beta‑lactamase detection were performed. Matrix‑assisted laser desorption ionization‑time‑of‑flight (MALDI‑TOF) was used for identification of species. Antibiotic susceptibilities of the isolates were detected by disk diffusion method. CTX‑M beta‑lactamase genes were investigated by polymerase chain reaction. Results: During the study period, a total of 1402 fecal samples were analysed with ESBL screening test and 490 Enterobacteriaceae strains isolated from these samples (Escherichia coli [n = 461, 94.1%], Klebsiella pneumoniae [n = 25, 5.1%], and Enterobacter cloacae [n = 4, 0.8%]). Fecal carriage of ESBL‑producing Enterobacteriaceae in the community was 34.3%. AmpC beta‑lactamases were detected in 26 (5.3%), and the frequency of CTX‑M was found as 96.9%. The resistance rates of the E. coli strains to fluoroquinolones, trimethoprim–sulfamethoxazole, and carbapenems were 31.2%, 33.3%, and 0%, respectively. Conclusion: The relative high prevalence of fecal carriage of ESBL‑producing bacteria in community warrants further study in this field including developing policies about antimicrobial use and close monitoring of resistancepatterns.Keywords: AmpC, cefotaxime‑M, Enterobacteriaceae, extended‑spectrum β‑lactamase, fecal carriag

Genotype distribution of Candida albicans isolates by 25S intron analysis with regard to invasiveness

The aim of this study was to genotype Candida albicans strains isolated from patients with invasive and non-invasive deep-seated infections. For this purpose, 301 C. albicans isolates (81 invasive and 220 non-invasive) were genotyped by using specific PCR primers designed to span the transposable group I intron of the 25S rDNA gene. Fifty-three of the 81 invasive isolates were genotype A (65.4%), eight were genotype B (9.9%) and 20 were genotype C (24.7%), while 98 of the 220 non-invasive isolates were genotype A (44.6%), 46 were genotype B (20.9%) and 76 were genotype C (34.5%). Genotype A was more prevalent among invasive isolates and genotypes B and C were more prevalent among non-invasive isolates (P = 0.0046). Genotypes D and E which represent C. dubliniensis were not found. These results indicate that there may be a relationship between C. albicans genotypes and invasiveness; genotype A being more invasive than others. The presence or absence of the transposable group I intron in the 25S rDNA gene may be important in determining the invasiveness of C. albicans

[Evaluation of blood culture practices: Use of system (Epicenter) data].

Sepsis is a serious clinical problem and estimated to be responsible for 18 million annual deaths worldwide. Therefore, the use and the rapid processing of blood cultures are important for the transition from empiric therapy to directed therapy. The aim of this study was to assess the best blood culture practices in Turkey. We have examined the collection practices and techniques at four different hospitals, and a total of 165.443 blood culture bottles were evaluated (2013-2015). At the preanalytical phase most of the data which were important and which could support hospital quality systems/practices were not entered into the HIS and EpiCenter system. At the analytical phase loading of the bottles and removal of positive bottles primarily occurred between 6:00 and 9:00 AM but the positivity rate of the bottles showed a homogeneous distribution throughout the day. In other words, there were significant delays at processing positive blood culture bottles related to laboratory workers. The effect of education regarding best practices, transition from single bottle to two bottle cultures was successful in all hospitals. Single bottle usage decreased below 10% in all hospitals. Significantly more positive cultures were detected at multiple cultures when compared with the single bottle collection practice. In retrospective patient records, it was seen that all the laboratories reported the results of Gram staining to the clinics. However, these data were not recorded to the EpiCenter. The contamination rates of Ankara Numune Hospital and Akdeniz University Faculty of Medicine Hospital are 6.2% and 5.4% respectively, contamination rates were not reported in other hospitals. The most common isolates detected in blood cultures were Escherichia coli, Klebsiella pneumoniae, Enterococcus faecium, Staphylococcus aureus, and Acinetobacter baumannii. The mean time for the detection of these organisms were less than 20 hours in the aerobic bottle and anaerobic bottles. A total of 79.6% of facultative anaerobic isolates were detected in both bottles; 9.8% were detected only in the aerobic bottles; 10.6% of the isolates were detected only in the anaerobic bottles. As a result, the educational efforts in Turkey have met with success for transition from collecting single bottle blood culture sets to two bottle blood cultures. However, further efforts are needed to increase the number of blood culture sets collected during a 24 hours' period. In addition, errors at the preanalytical, analytical and postanalytical periods (taking samples, loading bottles into the system and processing positive blood cultures) should be eliminated

Evaluation of Blood Culture Practices: Use of System (Epicenter) Data

Sepsis is a serious clinical problem and estimated to be responsible for 18 million annual deaths worldwide. Therefore, the use and the rapid processing of blood cultures are important for the transition from empiric therapy to directed therapy. The aim of this study was to assess the best blood culture practices in Turkey. We have examined the collection practices and techniques at four different hospitals, and a total of 165.443 blood culture bottles were evaluated (2013-2015). At the preanalytical phase most of the data which were important and which could support hospital quality systems/practices were not entered into the HIS and EpiCenter system. At the analytical phase loading of the bottles and removal of positive bottles primarily occurred between 6:00 and 9:00 AM but the positivity rate of the bottles showed a homogeneous distribution throughout the day. In other words, there were significant delays at processing positive blood culture bottles related to laboratory workers. The effect of education regarding best practices, transition from single bottle to two bottle cultures was successful in all hospitals. Single bottle usage decreased below 10% in all hospitals. Significantly more positive cultures were detected at multiple cultures when compared with the single bottle collection practice. In retrospective patient records, it was seen that all the laboratories reported the results of Gram staining to the clinics. However, these data were not recorded to the Epicenter. The contamination rates of Ankara Numune Hospital and Akdeniz University Faculty of Medicine Hospital are 6.2% and 5.4% respectively, contamination rates were not reported in other hospitals. The most common isolates detected in blood cultures were Escherichia coli, Klebsiella pneumoniae, Enterococcus faecium, Staphylococcus aureus, and Acinetobacter baumannii. The mean time for the detection of these organisms were less than 20 hours in the aerobic bottle and anaerobic bottles. A total of 79.6% of facultative anaerobic isolates were detected in both bottles; 9.8% were detected only in the aerobic bottles; 10.6% of the isolates were detected only in the anaerobic bottles. As a result, the educational efforts in Turkey have met with success for transition from collecting single bottle blood culture sets to two bottle blood cultures. However, further efforts are needed to increase the number of blood culture sets collected during a 24 hour's period. In addition, errors at the preanalytical, analytical and postanalytical periods (taking samples, loading bottles into the system and processing positive blood cultures) should be eliminated.C1 [Basustaoglu, Ahmet] Baskent Univ, Dept Med Microbiol, Fac Med, TR-06790 Ankara, Turkey.[Suzuk Yildiz, Serap] MoH Gen Directorate Publ Hlth, Dept Microbiol Reference Lab & Biol Prod, Ankara, Turkey.[Mumcuoglu, Ipek; Kursun, Senol] Ankara Numune Training & Res Hosp, Lab Med Microbiol, Ankara, Turkey.[Karahan, Zeynep Ceren; Evren, Ebru] Ankara Univ, Dept Med Microbiol, Fac Med, Ankara, Turkey.[Ogunc, Dilara; Ozhak Baysal, Betil] Akdeniz Univ, Dept Med Microbiol, Fac Med, Antalya, Turkey.[Kaleli, Ilknur; Demir, Melek] Pamukkale Univ, Dept Microbiol, Fac Med, Denizli, Turkey.[Murray, Patrick] BD Diagnost Syst, Hunt Valley, MD USA

The urgent need for microbiology literacy in society

Microbes and their activities have pervasive, remarkably profound and generally positive effects on the functioning, and thus health and well‐being, of human beings, the whole of the biological world, and indeed the entire surface of the planet and its atmosphere. Collectively, and to a significant extent in partnership with the sun, microbes are the life support system of the biosphere. This necessitates their due consideration in decisions that are taken by individuals and families in everyday life, as well as by individuals and responsible bodies at all levels and stages of community, national and planetary health assessment, planning, and the formulation of pertinent policies. However, unlike other subjects having a pervasive impact upon humankind, such as financial affairs, health, and transportation, of which there is a widespread understanding, knowledge of relevant microbial activities, how they impact our lives, and how they may be harnessed for the benefit of humankind – microbiology literacy – is lacking in the general population, and in the subsets thereof that constitute the decision makers. Choices involving microbial activity implications are often opaque, and the information available is sometimes biased and usually incomplete, and hence creates considerable uncertainty. As a consequence, even evidence‐based ‘best’ decisions, not infrequently lead to unpredicted, unintended, and sometimes undesired outcomes. We therefore contend that microbiology literacy in society is indispensable for informed personal decisions, as well as for policy development in government and business, and for knowledgeable input of societal stakeholders in such policymaking. An understanding of key microbial activities is as essential for transitioning from childhood to adulthood as some subjects currently taught at school, and must therefore be acquired during general education. Microbiology literacy needs to become part of the world citizen job description. To facilitate the attainment of microbiology literacy in society, through its incorporation into education curricula, we propose here a basic teaching concept and format that are adaptable to all ages, from pre‐school to high school, and places key microbial activities in the contexts of how they affect our everyday lives, of relevant Grand Challenges facing humanity and planet Earth, and of sustainability and Sustainable Development Goals. We exhort microbiologists, microbiological learned societies and microbiology‐literate professionals, to participate in and contribute to this initiative by helping to evolve the basic concept, developing and seeking funding to develop child‐friendly, appealing teaching tools and materials, enhancing its impact and, most importantly, convincing educators, policy makers, business leaders and relevant governmental and non‐governmental agencies to support and promote this initiative. Microbiology literacy in society must become reality