Antibacterial Resistance in Lower Respiratory Tract Bacterial Pathogens: A Multicenter Analysis from Turkey.

INTRODUCTION: This study aimed to evaluate the etiology of lower respiratory tract infections (LRTIs) and their antibiotic resistance. METHODOLOGY: Bacterial culture results of LRT samples from 17 hospitals between 2016-2019 were included in the study. All isolates were identified and AST were performed by automated microbiology systems. AST was performed according to EUCAST. RESULTS: Non-duplicate 30,051 (26,890 HA and 3156 CA) isolates detected as causative pathogen. LRTIs are caused by 85.1% Gram-negative bacterial pathogens and 14.9% Gram-positive. The most common isolates among HA pathogens were Acinetobacter spp. (27.4%), P.aeruginosa (22.2%), K.pneumoniae (17.9%); among CA pathogen S.pneumoniae (19.9%), P. aeruginosa (18.9%), H.influenzae (14.6%). ESBL rate was 62.5% in K.penumoniae; 53.1% in E.coli; 19.1% in Klebsiella spp; 13.9% in Enterobacter spp.; 8.6% in Proteus spp.; 6.3% in Citrobacter spp.; and 4.3% in Serratia spp. Resistance rates to carbapenems and colistin were 92.8% and 12.8% in A baumannii, 39.8% and 7.5% in P.aeruginosa, 47.3% and 18.5% in K.penumoniae. Among staphylococci, 27.3% of S. aureus and 82.4% of CoNS were methicillin resistant. 7.6% of E.faecium and 0.9% of E.faecalis were vancomycin resistant.  Linezolid resistant S. aureus, CoNS, E.faecalis and E.faecium rates were 0.3%, 2.9%, 0.0% and 4.6%. Inducible clindamycin resistant rate was 17.2% in S. aureus 38.2% in CoNS. Non-susceptible S.pneumoniae isolate rate to penicillin was 37.0%. 6.5% of S.maltophilia and 4.4% of B.cepacia isolates were resistant to trimethoprim/sulfamethoxazole. CONCLUSIONS: Antibiotic resistance was mainly observed among A.baumannii and K.pneumoniae and continuous surveillance of antimicrobial resistance patterns in the management of LRTIs is important.

[Investigation of various virulence factors among the hospital and community-acquired Staphylococcus aureus isolates by real-time PCR method]. / Hastane ve Toplum Kaynakli Staphylococcus aureus Izolatlarinda Çesitli Virülans Faktörlerinin Gerçek Zamanli PCR Yöntemiyle Arastirilmasi

Staphylococcus aureus is the most common cause of skin and soft tissue infections in the community and the most important cause of nosocomial infections. In this research, it was aimed to detect the presence of staphylococcal enterotoxin A to D (SEA, SEB, SEC and SED, respectively), toxic shock syndrome toxin-1 (TSST-1), Panton-Valentine leukocidin (PVL) and SCCmec phenotype in methicillin-resistant S.aureus (MRSA) isolates and to demonstrate the genotypic association between hospital acquired and community acquired isolates. In the study the virulence factors of 147 S.aureus strains isolated from various clinical samples at Gulhane Military Medical Academy Hospital Microbiology Laboratory between 2007 and 2010 were investigated by real-time polymerase chain reaction. MLVA (multiple locus variable number of tandem repeat analysis) method was used to demonstrate the genotypic association between hospital-and community-acquired isolates. Seventy-two (%48.9) of 147 S.aureus isolates were determined as community acquired and 75 (%51.1) as hospital acquired. Ninety-three (63.2%) isolates possesed at least one toxin (77 strains harboured one, and 16 strains harboured more than one). Of the isolates in which toxin was detected 59.1% (55/93) were hospital acquired, 40.9% (38/93) were community acquired. SEA was determined in 59 (40.1%), SEB in 8 (5.4%), SEC in 12 (8.1%), SED in 8 (5.4%), TSST- 1 in 17 (11.5%) and PVL in 6 (4.0%) of the isolates. Methicillin resistance was determined in 61.1% (44/72) of the hospital acquired isolates and 6.7% of the (5/75) community acquired isolates. In our study, SCCmec type III was detected in 90.9% (40/44) of hospital acquired MRSA isolates and SCCmec type IV in 40.0% (2/5) of community acquired MRSA isolates. Most of the strains (40/47; 85.1%) carrying SEA were hospital acquired, and they were determined as methicillin-resistant. According to MLVA, hospital and community acquired groups' clustering rates, number of clones, number of unique profile were determined as; 73.6% and 57.3%; 34% and 47%; 19% and 32%, respectively. It was concluded that high prevalence of SEA toxin in hospital acquired MRSA isolates indicated that there was a possible association between the presence of toxin and antimicrobial resistance.

[Resistance rates to major anti-tuberculosis drugs in Mycobacterium tuberculosis strains isolated from seven different regions of Turkey in 2003-2006 period]. / Ulkemizin yedi farkli bölgesinden 2003-2006 yillari arasinda izole edilen mycobacterium tuberculosis suslarinin majör antitüberkoloz ilaçlara direnç oranlari.

Multi-drug resistance in Mycobacterium tuberculosis (MDR-TB) is a global problem and has increased especially in areas where tuberculosis control programmes are inefficient. The aim of this study was to detect the resistance rates against isoniazide (INH), rifampisin (RMP), ethambutol (EMB) and streptomycin (SM) in M. tuberculosis strains collected from 7 different regions including 62 cities and sent to Refik Saydam Hygiene Center National Tuberculosis Reference and Research Laboratory. Of the patients included, 7.61% were children, 92.39% were adults; 76.16% were male and 23.84% were female. These strains were isolated from sputum (n = 885, 81.11%), gastric lavage (n = 49, 4.49%), pleural fluid (n = 43, 3.94%), urine (n = 30, 2.74%), bronchoalveolar lavage (n = 22, 2.01%), and other clinical samples (n = 62, 8.46%) such as cerebrospinal fluid, lymph node, abscess material, lung tissue. The susceptibilities of the 1091 M. tuberculosis strains against the major anti-tuberculosis drugs were determined by the proportion method in Lowenstein-Jensen medium. Three hundred ninety two of the isolates were from Central Anatolia, 146 from Black Sea, 419 from Aegean, 28 from Mediterranean, 20 from Marmara, 64 from Eastern Anatolia and 21 from South Eastern Anatolia regions of Turkey. The distribution of the strains according to years were as follows: 88 in 2003, 114 in 2004, 341 in 2005 and 548 in 2006. Resistance to at least one of the drugs tested was found in 264 (14.20%) strains. Overall drug resistance rates to INH, RMP, EMB and SM were 12.3%, 10.1%, 6% and 15.8%, respectively. MDR-TB rate was 10% for this 4 years study period. MDR-TB rate was detected as 13.2%, 9.7%, 10.1% and 9.6% in children, adult, male and female patients, respectively. MDR-TB rate did not exhibit a statistically significant difference in terms of sex, age and study years (p > 0.05). However, this rate showed statistically significant difference in terms of geographical regions (p < 0.05). This study emphasized that regular surveillance of M. tuberculosis resistance to the major anti-tuberculosis drugs will provide valuable data for the effective national control and treatment of tuberculosis.

[An outbreak of vanA genotype Enterococcus faecium in pediatric clinic of a training hospital]. / Bir egitim hastanesinin çocuk kliniginde vanA genotip Enterococcus faecium salgini.

Vancomycin-resistant enterococci (VRE) have been increasingly reported from most countries around the world following initial isolation from patients in United States and European countries. A vancomycin-resistant Enterococcus faecium (VREF) outbreak was determined by hospital infection control committee in the pediatric unit of Gulhane Military Medical Academy, Ankara, Turkey in the first week of March 2008. While one of the 4 VREF strains was isolated from urine culture of a patient with neuroblastoma, the remaining strains were isolated from cultures of urine and rectal swab samples of a patient with nephrotic syndrome and from the hospital room doorknob of this patient. Aims of this study were to determine antibiotic susceptibilities by E-test, to investigate the presence of vanA, vanB and vanC-2 resistance genes by polymerase chain reaction (PCR), and to genotype the 4 strains by pulsed field gel electrophoresis (PFGE) and repetitive PCR (rep-PCR) (DiversiLab, bioMérieux, France). All isolates conferred high level [minimum inhibitor concentration (MIC) > 256 mg/L] vancomycin and teicoplanin resistance by E-test method. The isolates were also found resistant to gentamicin, streptomycin, ampicillin, erythromycin, penicillin and were susceptible to tetracycline and linezolid. The vanA gene was detected in all strains by PCR. It was demonstrated that the 4 VRE strains belonged to a single clone as shown by both PFGE and rep-PCR methods. Prompt and accurate detection of VRE and determination of the genotypes is of crucial importance to prevent horizontal transfer of the strains in the hospital. When compared with PFGE, the DiversiLab commercial rep-PCR seems to be a reliable and more rapid method to detect the genetic relationship between strains leading to an outbreak.

[Genotypic characteristics of Neisseria meningitidis serogroup W-135 strains isolated as the agent of fatal meningitis in a military hospital]. / Bir askeri hastanede fatal menenjit etkeni olarak izole edilen Neisseria meningitidis serogrup W-135 suslarinin genotipik özellikleri.

The aim of this study was to describe the genetic characterization of a total of 6 Neisseria meningitidis serogroup W-135 strains isolated from patients with meningitis and carriers in a military hospital in 2007-2008. Suspected colonies on modified Thayer-Martin medium plates were screened for oxidase reactivity and Gram stain. If gram-negative diplococci were present, a biochemical profile by the API NH system was used for species confirmation. Pulse field gel electrophoresis typing of Nhel-digested DNA was performed by a previously described method. Multi-locus sequence typing (MLST) was performed using the standard primers as listed on the Neisseria MLST website. Three distinct sequence types (STs) were identified: ST-11, ST-2754, ST-3751. One of the clinical isolates was identified as the same sequence type with Hajj isolate (ST-11) and the isolate with ST-2754 was the same as the first Turkish clinical strain isolated in 2003. These data demonstrated that along with ST-11 which is a known Hajj isolate, the ST-2754 strain causing meningococcal disease in Turkey beginning from the year 2003, should be carefully monitored.

[Investigation of the presence and subgroups of adenoviruses in nasopharyngeal samples of military recruits with respiratory tract infections]. / Solunum yolu enfeksiyonu olan askerlerin nazofarengeal örneklerinde adenovirus varliginin ve alt gruplarinin arastirilmasi.

Adenoviruses (AdV) are important pathogens primarily associated to respiratory infections of children and military staff even though it is also associated to many clinical manifestations, such as cystitis, conjunctivitis, diarrhea, hepatitis, myocarditis, and encephalitis. The goals of this study were to detect and type acute respiratory disease associated AdV isolates among military trainees in a selected region without an evidence of an outbreak. Throat swab samples were obtained during February 2006-March 2006 period, from 180 military male trainees aged 20-29, who were presented with respiratory tract symptoms and an oral temperature of > or = 38.0 degrees C. All specimens were tested by HEp-2 cell culture and real-time TaqMan PCR with AdV specific primers and probes. Positive cell culture results, presented as AdV-specific cytopathic effects, were confirmed by real-time polymerase chain reaction (PCR). AdV subgroup differentiation were performed using conventional PCR assays with the primer set specific for subgroup B, C or E. Subgroup specific PCR products were restricted with Mspl enzyme in order to check whether they were specific or not. AdV positivity was detected in 8 (4.4%) samples by cell culture and in 9 (5.0%) by the real-time PCR. All culture positive samples were also positive by real-time PCR. Eight of the nine real-time PCR-positive specimens were found to be in the subgroup E (this group contains only AdV type 4) and the results were confirmed with restriction enzyme analysis. One isolate could not be typed with the available primers. These data indicated that both real-time TaqMan PCR and restriction enzyme analysis provide sensitive and specific tools for AdV detection and subgroup differentiation for throat swab specimens. It can be concluded that since the prevalence of AdV infections was low in the study group, AdV infections were not considered as a vaccine requiring health problem in Turkish armed forces, however, larger scale studies were needed to reach a more precise conclusion.