Alpha variant (B.1.1.7) of SARS-CoV-2 increases fatality-rate for patients under age of 70 years and hospitalization risk overall.

The emergence of new SARS-CoV-2 variants is a challenge to the control of this pandemic. It is therefore important to collect and to analyze data related to the infection caused by different variants. We have obtained more than 3,700 COVID-19 patients between April 2020 and March 2021 from Tokat, Turkey (roughly 3,100 outpatients and close to 600 inpatients) where about 30% were infected with Alpha variant (B.1.1.7). Descriptive statistics was used to characterize different subgroups. Both logistic regression and cause-specific Cox survival analysis of competing-risk was run on inpatients, to examine the impact of Alpha variant on hospitalization, on mortality and on other factors. We observed that the Alpha variant is over-represented in inpatients than outpatients so infection by Alpha variant increases the chance for hospitalization. The impact of Alpha variant on mortality seems to depend on the patient's age. For patients under age of 70, the case-fatality-rate was 0.84% (5.3%) for patients without (with) Alpha variant (Fisher's test P-value = 2.4 × 10-10). For patients above age of 70, the trend is opposite: the case-fatality-rate is 31.5% (13.6%) for patients without (with) Alpha variant (Fisher's test P-value = 0.0016). The two opposite trends would cancel each other, making other analyses such as cause-specific Cox regression and logistic regression non-significant. The Alpha variant increases the risk for hospitalization, increases the case-fatality-rate for lower age group, and decreases the case-fatality-rate for the upper age group. If the increase of case-fatality-rate in not the most senior group holds true, it should provide useful information for a vaccination planning to counter the impact of Alpha variants.

[Characterization of class 1 and class 2 integron gene cassettes in Escherichia coli strains isolated from urine cultures: a multicenter study]. / Idrar kültürlerinden izole edilen Escherichia coli suslarinda sinif 1 ve sinif 2 integron gen kasetlerinin karakterizasyonu: Çok merkezli bir çalisma.

Escherichia coli is the most common pathogen isolated from both nosocomial and community acquired urinary tract infections. Although there are many studies from different centers concerning the antibiotic susceptibility of E.coli isolates in Turkey, the studies are quite few about class 1 and class 2 integron cassettes in clinical E.coli isolates from urinary samples. The aim of the study was to investigate the antibiotic susceptibility and the carriage of integron gene cassettes in E.coli strains isolated from urinary samples. A total of 626 E.coli strains isolated from urine cultures in microbiology laboratories located at 10 provinces from different regions of Turkey (Denizli, Ankara, Kayseri, Nigde, Sanliurfa, Kahramanmaras, Tokat, Malatya, Konya and Trabzon) between June 2011-June 2012 were included in the study. The identification and antibiotic susceptibility testing of the isolates were studied by conventional methods as well as Vitek® 2 Compact (bioMérieux, France) and BD Phoenix™ 100 (Becton Dickinson, USA) systems. The antibiotic susceptibilities of all the isolates were retested by Kirby-Bauer disk diffusion method according to CLSI recommendations in the main center of the study in order to achive the standardization. The presence of integrons was detected with polymerase chain reaction (PCR) method by using specific primers targeting class 1 (intI1) and class 2 (intI2) integrase gene regions. After integron amplification the samples were cloned and subjected to DNA sequencing. When the antibiotic susceptibility of the isolates were evaluated, the highest resistance was observed against most commonly used empirical antibiotics namely ampicillin and trimethoprim-sulfamethoxazole (SXT) with the mean rate of 58.6% (range: 43.8%-73.2%) and 41.2% (range: 35.4%-45.8%), respectively. The most effective antibiotics detected against the isolates were imipenem and amikacin with the lowest resistance rates of 0.2% (range: 0%-1.1%) and 0.6% (range: 0%-3.2%), respectively. The frequency of positive IntI1 gene and class 1 integron gene cassettes were found as 25.8% (162/626) and 16.6% (104/626), respectively, whereas the frequency of positive intI2 gene II and class 2 integron gene cassettes were 5.1% (32/626) and 3% (19/626), respectively. The lowest intI1 gene frequency was detected in the isolates from Kayseri (16.6%) and the highest in the isolates from Kahramanmaras (35.4%) provinces. While there was no intI2 gene in the isolates from Denizli and Kayseri, the highest frequency was 12.1% in the isolates from Sanliurfa province. dfrA1 gene, the most frequent gene among integron gene cassettes was positive in 31 class 1 integron gene cassette alone, and positive with aadA1 gene in 18 class 1 integron gene cassettes. dfrA1 gene was positive with aadA1a just in one isolate. dfrA17 allele was positive in one isolate alone, in 28 isolates with aadA1, and in 15 isolates with aadA5. aadA1 gene was detected in four isolates. dfrA17-sat-aadA5 co-existence was detected among class 2 integron gene cassette in isolates from six provinces. dfrA1-sat-aadA1 was detected in one isolate from Ankara province and dfrA1 was detected in one isolate in Nigde province only. As a result, dfrA1 and aadA1 genes are the most common types of genes among class 1 and class 2 integron gene cassettes in E.coli isolated from urine cultures. It was concluded that high resistance against streptomycin (31.2%) and SXT (41.2%) supported the dissemination of integron-mediated genes dfr, sul1 and aad in the isolates.

[Investigation of the frequency and distribution of beta-lactamase genes in the clinical isolates of Acinetobacter baumannii collected from different regions of Turkey: a multicenter study]. / Türkiye'nin farkli bölgelerinden toplanan klinik Acinetobacter baumannii izolatlarinda beta-laktamaz gen sikligi ve dagiliminin arastirilmasi: Çok merkezli bir çalisma.

The diversity and distribution of TEM, SHV and CTX-M type of extended-spectrum beta-lactamases (ESBLs) are important for the treatment and control of infections. Determination of ESBL genes in clinical isolates by polymerase chain reaction (PCR) and DNA sequencing can obtain useful data for their molecular epidemiology and risk. The aim of this study was to investigate the frequency of beta-lactamase genes in Acinetobacter baumannii strains isolated from different regions of Turkey. A total of 519 A.baumannii strains collected from hospitals located at 12 different provinces of Turkey (Bolu (n= 67), Tokat (n= 47), Trabzon (n= 25), Ordu (n= 27), Diyarbakir (n= 47), Nigde (n=31), Kayseri (n= 36), Ankara (n= 41), Kirikkale (n= 26), Kahramanmaras (n= 25), Mersin (n= 40), Istanbul (n= 107)] between 2011-2012 period were included in the study. Identification of the isolates were performed by both conventional methods and automated systems, VITEK2 Compact (BioMerieux, France) and API 32GN (BioMerieux, France). Disc diffusion method was used for the detection of antibiotic susceptibilities of the isolates and the results were evaluated according to CLSI (Clinical and Laboratory Standards Institute) criteria. Tigecycline and colistin sensitivities of the isolates were evaluated according to BSAC (British Society for Antimicrobial Chemotherapy) criteria. The presence of beta-lactamase genes, namely blaoxa-51, blaTEM, blaSHV, blaCTX-M1, blaCTX-M2, blaGES and blaVIM were detected by PCR. In our study, the resistance rates against colistin, tigecycline, ampicillin-sulbactam, amoxicillin-clavulanic acid, cefoperazone/sulbactam, tobramycin, ceftriaxone, piperacillin-tazobactam, gentamicin, ampicillin, tetracycline, cefepime, piperacillin, amikacin, trimethoprim-sulfamethoxazole, meropenem, levofloxacin, ciprofloxacin, imipenem and ceftazidime were detected as; 0.6%, 2.7%, 11.9%, 15.2%, 21%, 22.9%, 23.9%, 48.6%, 59.5%, 61.8%, 66.3%, 67.8%, 69.2%, 71.1%, 77.5%, 78.6%, 81.1%, 82.9%, 87.5% and 89.4%, respectively. All of the isolates (100%) were OXA-51 positive, while 443 (85.4%) out of 519 strains harbored other beta-lactamase genes searched in the study. When the distribution of the genes were evaluated, blaTEM-1 was found as the predominant one with a frequency rate of 55.7% (n=289/519), followed by blaCTX-M2 (63/519, 12.1%), blaCTX-M1 (42/519, 8.1%), blaSHV (40/519, 7.7%), blaGES (8/519, 1.5%) and blaVIM (1/519, 0.2%). Cooccurence of ESBL genes was detected in 16.3% (72/443) of the strains, being mostly TEM+CTX-M2 (20/72, 27.8%), TEM+SHV (11/72, 15.3%) and TEM+CTX-M1 (10/72, 13.9%). In addition, it was noted that the distribution of ESBL genes between isolates showed differences according to the provinces. Accordingly, none of the strains isolated from four provinces (Bolu, Nigde, Mersin, Kahramanmaras) and from three provinces (Bolu, Kahramanmaras, Diyarbakir) harbored blaCTX-M1/M2 and blaSHV genes, respectively. The blaTEM gene was detected in isolates collected from all of the provinces, with a highest frequency in Nigde (28/31, 90.3%) and lowest in Trabzon (1/25, 4%). The presence of GES-11 type ESBLs was found only in the isolates sent from Nigde province (8/31; 25.8%). Screening of metallo-beta-lactamase VIM gene also yielded a single positive result amongst only Nigde isolates (1/31; 3.2%), and this gene was identified as VIM-5 type by DNA sequencing. This study which is the first comprehensive national research to characterize ESBLs in A.baumannii isolates by molecular methods, showed that the most prevalent ESBL type is TEM (289/519, 55.7%) amongst A.baumannii strains isolated from different regions of our country. The data of our study is parallel to the results of previous studies carried out from Turkey.

Detection of class 1 integron in Acinetobacter baumannii isolates collected from nine hospitals in Turkey.

OBJECTIVE: To investigate the antibiotic resistance genes inserted into class 1 and class 2 integrons in Acinetobacter baumannii (A. baumannii) isolates obtained from nine different cities in Turkey. METHODS: A collection of 281 A. baumannii clinical isolates were collected from nine diferent state hospitals in Turkey and were confirmed as A. baumannii by conventional biochemical, API testing and bla-OXA-51 specific PCR. The isolates were examined by PCR for existence of class 1 and 2 integron gene cassettes. RESULTS: They were characterized by antimicrobial susceptibility testing and the highest resistance rates were determined for piperacillin (90.03%), ciprofloxacin (87.54%), cefepime and trimethoprim/sulfamethoxazole (81.13%). The lowest resistance rates was for cefotaxime (3.55%). class I integrons were detected in 6.4% (18/281) of A. baumannii strains and no class 2 integron was detected. The gene cassettes of class 1 integrons AacC1-AAC(3)I-aadA1, AacC1-aadA1, AAC(3)-I, AAC(3)-I -AAC(3)-I -aadA1, TEM-1, AAC(3)-I-aadA1 - AAC(3)-I -AAC(3)-I, AAC(3)-I -AAC(3)-I -AAC(3)-I -aadA1, AAC(3)-I - aadA1, AAC(3)-I-AAC(3)-I, AAC(3)-I-aadA1- AAC(3)-I-aadA1, AAC(3)-I- AAC(3)-I- aadA1-AAC(3)-I-aadA1 were detected in eighteen strains. The aac genes family were most frequently found integrated into the class 1 integrons and it was followed by aadA genes and TEM-1 genes. CONCLUSIONS: This is an extensive study on the distribution of class 1 integron among A. baumannii in Turkey. In addition to these, two new alleles were observed. Their percentage rates of similarity to other cassettes are 95% aadA1 ( TKA18) and 89% aadA1 (ANKA3).