Multidrug resistance in pathogens of community-acquired urinary tract infections in Turkey: a multicentre prospective observational study

BACKGROUND: To have country-wide information about multidrug resistance (MDR) in isolates from community-acquired urinary tract infections (CAUTI) of Turkey, in terms of resistance rates and useful options. METHODS: We used a geocode standard, nomenclature of territorial units for statistics (NUTS), and a total of 1588 community-acquired isolates of 20 centres from 12 different NUTS regions between March 2019 and March 2020 were analysed. RESULTS: Of the 1588 culture growths, 1269 (79. 9%) were Escherichia coli and 152 (9.6%) were Klebsiella spp. Male sex, advancedage, and having two or more risk factors showed a statistically significant relation with MDR existence (p < 0.001, p: 0.014, p < 0.001, respectively) that increasing number of risk factors or degree of advancing in age directly affects the number of antibiotic groups detected to have resistance by pathogens. In total, MDR isolates corresponded to 36.1% of our CAUTI samples; MDR existence was 35.7% in E. coli isolates and 57.2% in Klebsiella spp. isolates. Our results did not show an association between resistance or MDR occurrence rates and NUTS regions. DISCUSSION: The necessity of urine culture in outpatient clinics should be taken into consideration, at least after evaluating risk factorsfor antibacterial resistance individually. Community-acquired UTIs should be followed up time- and region-dependently. Antibiotic stewardship programmes should be more widely and effectively administrated.

Analyses of Plasmids Harbouring Quinolone Resistance Determinants in Enterobacteriaceae Members.

The aim of this study was to explore the plasmid characteristics of eight clinical Enterobacteriaceae strains containing extended broad spectrum beta-lactamases and plasmid-mediated quinolone resistance. Plasmids were transferred by conjugation or transformation and resistance determinants were investigated by PCR. We showed that at least one plasmid harbouring qnrB or qnrS determinant was transferred by conjugation in five isolates. QepA determinant was confirmed to be on a non-conjugative plasmid. We found at least one beta-lactamase gene in seven of the eight clinical isolates having plasmid-mediated quinolone resistance, which indicated that these two resistance determinants were mostly on the same conjugative plasmids.

[Comparison of phenotypic methods and polymerase chain reaction for the detection of carbapenemase production in clinical Klebsiella pneumoniae isolates]. / Klinik Klebsiella pneumoniae izolatlarinda karbapenemaz üretiminin saptanmasinda polimeraz zincir reaksiyonu ve fenotipik yöntemlerin karsilastirilmasi.

Being a member of the Enterobacteriaceae family, Klebsiella pneumoniae is an opportunistic pathogen that inhabits normal human microbiota and causes predominantly hospital-acquired infections. The emergence of K.pneumoniae isolates which are resistant particularly to the carbapenem group of antibiotics has led to an increase in hospitalization period, mortality and morbidity. Although different rates of resistance are observed between countries, regions and even healthcare facilities, there has been a rapid increase in the prevalence of carbapenem-resistant strains in the last 10 years. Fast and correct identification of carbapenem-resistant strains is important for the successful treatment of infections caused by these resistant bacteria. The objective of this study was to investigate the presence and the types of carbapenemases in carbapenem-resistant K.pneumoniae strains using "MASTDISCS™ ID carbapenemase detection disc set", a commercial product that can be used for this purpose, and "Carbapenem Inactivation Method (CIM)", a relatively new method, and compare the results of these methods by polymerase chain reaction (PCR). For this purpose, we used 54 K.pneumoniae strains isolated in 2015-2016, that were resistant to any of the ertapenem, meropenem or imipenem antibiotics. The identification of the strains was performed using VITEK MS and their antibiotic susceptibility tests were carried out using the VITEK 2 Compact® automated system. For the strains that were found resistant to carbapenems in the automated system, the minimum inhibitor concentration (MIC) values were determined by the gradient testing method according to the recommendations of "The European Committee on Antimicrobial Susceptibility Testing (EUCAST)". The blaOXA-48, blaIMP, blaNDM, blaVIM, and blaSIM genes were investigated with PCR among these isolates. Phenotypic enzyme typing was performed in the carbapenem-resistant strains using the "MASTDISCS™ ID carbapenemase detection disc set" and "Carbapenem Inactivation Method (CIM)". REP-PCR was used to reveal clonal relationship of the isolates. The 54 K.pneumoniae isolates were found as resistant to carbapenem and the MIC50 and MIC90 values of imipenem, meropenem and ertapenem were 32 µg/ml. Only 33 of the strains had blaOXA-48 and two of them had only blaNDM, the remaining 19 strains had both of these two genes. The blaIMP, blaVIM and blaSIM genes were not encountered in any of the isolates. When the isolates were assessed by the REP-PCR method, six main clones were detected. The "MASTDISCS™ ID carbapenemase detection disc set" was able to detect all the carbapenemase producing strains and it remained incapable of distinguishing OXA-48 in the strains which had both OXA-48 and metallo beta lactamase (MBL) enzymes. The CIM method showed a low rate of positivity (46.15%) in the strains containing blaOXA-48, but was found much more successful in the strains containing blaNDM with a detection rate of 85.71%. In this study, it was concluded that the Mastdiscs-ID method could be successfully used to detect the presence of blaOXA-48 which has a high prevalence in our country.

Investigation of class-d beta-lactamases causing carbapenem resistance in clinical Acinetobacter baumannii isolates

Background/aim: Acinetobacter baumannii is an important causative agent of nosocomial infections, and carbapenems have been frequently used in the treatment of these infections. This study was designed to investigate the prevalence of primary carbapenem hydrolyzing oxacillinase (CHO) types in clinical A. bumannii strains. Materials and methods: Minimum inhibitory concentration (MIC) values of 76 imipenem nonsusceptible A. baumannii strains, isolated from a tertiary care hospital, were determined by microdilution method. The clonal relationship of the isolates was analyzed with enterobacterial repetitive intergenic consensus (ERIC)-PCR, and the presence of CHO major groups (OXA-23; OXA-24, OXA-51, and OXA-58 groups) was investigated with multiplex PCR. Results: According to the ERIC-PCR patterns, the isolates were distributed in 13 different clones, the largest of which had 40 members. blaOXA-51-group was detected in representatives of all clones, whereas blaOXA-23-group was detected in representatives of all but two small clones. Additionally, the presence of blaOXA-58-group was discovered in the members of two small clones, whereas blaOXA-24-group was not encountered in any of the examined strains. Conclusion: Molecular fingerprinting revealed that most imipenem-resistant A. baumannii strains were clonally related. blaOXA-23-group and blaOXA-51-group were mostly responsible for the imipenem resistance of the examined A. baumannii strains.

Antibacterial resistance patterns and incidence of hospital-acquired Staphylococcus aureus bacteremia in a tertiary care educational hospital in Turkey: a perspective from 2001 to 2013

Background/aim: Staphylococcus aureus is an important nosocomial pathogen and a successful antimicrobial-resistance developer. In this study we retrospectively evaluated the resistance patterns and incidence of microbiologically confirmed nosocomial bacteremia (MCNB) related S. aureus strains between 2001 and 2013. Materials and methods: Any patient in whom S. aureus was isolated in at least one set of blood cultures (sent to the bacteriology laboratory 72 h after hospital admission) was considered to have MCNB. Results: The methicillin-resistant S. aureus (MRSA) rate in 2001 was 73.8% whereas it was 36.2% in 2013. When the 2001-2003 and 2011?2013 periods were compared, resistance to oxacillin, levofloxacin, gentamicin, erythromycin, and clindamycin decreased significantly (P < 0.05). When we evaluated the total S. aureus, MRSA, and methicillin-sensitive S. aureus (MSSA) bacteremia rates per 1000 days and 1000 patients, there was an increase in the 2004?2005 period, which was followed by a slight decrease until 2013 (P < 0.05). There was a plateau in MCNB-related S. aureus rates between 2008 and 2011. Conclusion: There was a decrease in overall S. aureus and MRSA bacteremia incidence as well as MRSA rates except for a plateau between 2008 and 2011. This steady decrease in the resistance rates is most probably due to the 2003 budget application and application of antimicrobial stewardship.

Evaluation of antibody responses in healthcare workers before & after meningococcal vaccine and determination of meningococcal carriage rates.

The rates of nasopharyngeal meningococcal carriage in healthcare workers are unknown. Meningococcal vaccine is recommended for risk groups but healthcare workers are not included in risk groups for many countries. Herein, we aimed to investigate the nasopharyngeal meningococcal carriage rates, basal and after one dose of Men-ACWY-DT vaccine response on the 30th day by evaluating meningococcus IgG antibody levels and decolonization at month six after vaccination among the detected carriers. Nasopharyngeal swab samples were taken before vaccination to evaluate meningococcal carriage in healthcare workers. All participants received a single dose of Men-ACWY-DT vaccine. Serum samples were collected immediately before vaccination and again on day 30 post-vaccination. Antibodies in the stored sera were analyzed using the ELISA method. Participants who were determined to carry meningococci at the initial visit underwent another round of nasopharyngeal swab tests six months post-vaccination to check for decolonization. Between November 2020 and May 2021, we evaluated samples from 100 physicians [52 % females, 28.28 ± 4.45 (min: 24, max: 49)]. The majority of the physicians worked in the emergency department (45 %), followed by the infectious diseases clinic (14 %). Fifty-eight physicians had a history of at least one contact with a meningococcus-infected patient, and 53 (91.4 %) had used prophylactic antibiotics at least once due to this exposure. None of the study group nasopharyngeal swab cultures were positive for Neisseria meningitidis. Before the Men-ACWY-DT vaccine, anti-meningococcus IgG positivity was detected in the serum samples of only 3 (3 %) participants. By day 30 after vaccination, 48 % of participants showed positive for antibodies. As we didn't detect nasopharyngeal carriage in any participants, we didn't evaluate decolonization among carriers six months post-vaccination. Notably, detection of antibodies was evident in about half of the participants on day 30 after receiving a single dose of the Men-ACWY-DT vaccine.

Serotype distribution of Streptococcus pneumoniae and pneumococcal vaccine coverage in adults in Turkey between 2015 and 2018.

OBJECTIVE: To evaluate the serotype distribution and antibiotic resistance in pneumococcal infections in adults and to provide a perspective regarding serotype coverage of both current and future pneumococcal vaccines. PATIENTS AND METHODS: This passive surveillance study was conducted with the Streptococcus pneumoniae strains isolated from the specimens of patients with pneumonia (materials isolated from bronchoalveolar lavage), bacteraemia, meningitis, pleuritis and peritonitis between 2015 and 2018. Serogrouping and serotyping were performed by latex particle agglutination and by conventional Quellung reaction using commercial type-specific antisera, respectively. The strains were analysed for penicillin, cefotaxime, erythromycin and moxifloxacin susceptibilities by E-test. RESULTS: In the whole study group (410 samples from adults aged ≥18 years), the most frequent serotypes were 3 (14.1%), 19 F (12%) and 1 (9.3%). The vaccine coverage for PCV13, PCV15, PCV20 and PPV23 was 63.9%, 66.6%, 74.1% and 75.9%, respectively, in all isolates. Penicillin non-susceptibility in invasive pneumococcal disease (IPD) was 70.8% and 57.1% in the patients aged <65 and ≥65 years, respectively. About 21.1% and 4.3% of the patients with and without IPD had cefotaxime resistance. Non-susceptibility to erythromycin and moxifloxacin was 38.2% and 1.2%, respectively. CONCLUSIONS: The results revealed that novel PCV vaccines may provide improved coverage as compared with the currently available vaccine, PCV13. The significant antibiotic resistance rates imply the need to extend the serotype coverage of the vaccines. Continuing the surveillance in pneumococcal diseases is critical to explore the serotype distribution and incidence changes of IPD cases in the population and to inform policy makers to make necessary improvements in the national immunization programmes.Key messagesThis multicentre study demonstrated the most recent serotype distribution and antibiotic resistance in adult population in Turkey.Shifting from PCV13 to novel conjugated vaccines will significantly increase the coverage.Continuing the surveillance in pneumococcal diseases is critical to explore the serotype distribution changes and the incidence of cases with invasive pneumococcal disease in the population.

Comparison of Culture-Positive and -Negative Microbial Keratitis

Objectives: To evaluate and compare the risk factors, presenting features, and outcomes of patients with culture-positive and culture-negative microbial keratitis (MK) who presented to a tertiary referral center. Materials and Methods: We conducted a retrospective review of the medical records of 314 patients who were diagnosed with MK in our clinic between 2012 and 2019. Results: Among 314 patients, 142 had positive cultures (45.2%). The mean ages of the culture-positive and -negative patients at the time of diagnosis were 51.39±21.31 (range, 14-90) years and 56.68±21.34 (7-94) years, respectively (p=0.028). The mean best corrected visual acuity (BCVA) of the culture-positive and -negative patients were1.74±1.25 (0-3.1) LogMAR and 1.91±1.23 (0-3.1) LogMAR prior to treatment and increased to 1.21±1.30 (0-3.1) LogMAR and 1.27± 1.29 (0-3.1) LogMAR at last visit, respectively. There was no statistically significant difference between culture-positive and -negative patients' BCVA levels at presentation or last visit. Ninety-two patients (64.7%) were infected with bacteria and 50 patients (35.2%) with fungi. The most common pathogen was Pseudomonas aeruginosa (18.3%), followed by Streptococcus pneumoniae (11.2%) and Fusarium spp. (11.2%). Keratitis foci were either centrally or paracentrally located in 105 eyes (73.9%) of culture-positive patients and 149 eyes (86.6%) of culture-negative patients. Multiple foci were present mostly in culture-positive patients (p=0.001). There was no significant difference between the culture-positive and -negative groups in terms of hypopyon presence (p=0.364). The proportion of contact lens (CL) wearers was 33% (n=47) among culturepositive MK patients and 13.3% (n=23) among culture-negative MK patients, respectively (p<0.001). Culture positivity was found to be significantly higher in keratitis associated with CL use (p=0.0001). Conclusion: Microbiological analysis and culture evaluation are important steps in order to manage proper treatment in microbial keratitis. Prognosis mostly depends on the infectivity of the microbiological agent.

Silencing acpP gene via antisense oligonucleotide-niosome complex in clinical Pseudomonas aeruginosa isolates.

Pseudomonas aeruginosa, an opportunistic Gram-negative pathogen, is one of the major causes of nosocomial infections. In addition to its physiological adaptation capacity, it can develop resistance to disinfectants and antibiotics through various mechanisms. Recently, new eradication methods are gaining attention. Therefore, in this study, an LNA-2'-O-methyl hybrid antisense oligonucleotide targeting the acyl carrier protein P (acpP) gene was introduced into P. aeruginosa isolates. The design was determined through sequence analysis and prediction of the secondary structure of mRNA by software. Niosomes were used for enhancing cellular uptake. The control of the binding and transfection ability of the sequence was determined fluorometrically by labeling with 6-Fam. The effects were determined with broth microdilution method and qPCR studies. Eight different formulations were prepared. Among these, one formulation has shown to have ASO complexation ability whose composition was 312 µl Span 80 + 69.5 mg Cholesterol+ 36.4 mg CTAB+1 ml Chloroform and 5 ml dH2O. Thus this formulation was determined as the delivery system for the next stages. Significant gene inhibition was detected at the six isolates. Results of this study suggested that niosomes can be used as a delivery system for cellular uptake of ASO and could eliminate bacterial growth.

Effects of disinfectants and ciprofloxacin on quorum sensing genes and biofilm of clinical Pseudomonas aeruginosa isolates.

BACKGROUND: Pseudomonas aeruginosa is one of the most virulent bacteria and quorum sensing (QS) genes have an importance on virulence factors such as biofilm that provide resistance against disinfectants and antibiotics. OBJECTIVE: This study aimed to determine the minimum inhibitory concentrations of the disinfectants, to investigate the effects of disinfectants and ciprofloxacin on biofilm production mature biofilm of clinical P. aeruginosa isolates, and it was aimed to investigate the effects of the agents on the expression levels of several QS-related genes in the isolates. METHODS: Minimum inhibitory concentration (MIC) levels of polyhexamethylene biguanide (PHMB), chlorhexidine (CHX), quaternary ammonium compounds (QAC), glutaraldehyde (GLU) and ciprofloxacin (CIP) against clinical P. aeruginosa isolates were evaluated by microdilution method. Effects of the agents on the biofilm producing capacities of clonally unrelated nine strains were investigated by spectrophotometric method. Alterations in the expression of QS-related genes (lasI, lasR, rhlI and rhlR) were investigated by qPCR in three isolates that were CIP-susceptible and strong biofilm producer. RESULTS: According to microdilution method results, three isolates were found as resistant, one isolate was found as intermediate susceptible and five isolates were found as susceptible to CIP, and CHX (7.81-31.25 µg/mL) had the lowest MIC against P. aeruginosa. CHX inhibited biofilm production levels of eight of nine isolates, and GLU and CIP inhibited six of nine isolates in the presence of agents at MIC levels. GLU inhibited the mature biofilm levels of three of nine isolates at MIC and MIC/4 levels and four of nine isolates at MIC/2 levels. Expression levels of QS-related genes were reduced or induced in the presence of different disinfectants. CONCLUSIONS: More efforts are required to decrease the risk of ineffective and low-dose application of disinfectants and antimicrobials against bacteria. Targeting of QS-related genes may be a reasonable strategy for the inhibition of virulence factors in P. aeruginosa.

Investigation of the Antimicrobial Susceptibility Profile, Virulence Genes, and Epidemiologic Relationship of Clinical Salmonella Isolates.

OBJECTIVES: The objectives of this study were to investigate the epidemiologic relationship, prevalence of the beta-lactamase and virulence genes of clinical ampicillin-resistant Salmonella enterica. MATERIALS AND METHODS: In vitro ampicillin susceptibilities of 117 Salmonella enterica isolates obtained between 2011-2012 from Ege University Hospital, Bacteriology Laboratory of Medical Microbiology Department were examined using disc diffusion assays in accordance with the CLSI guidelines. The MIC levels in the ampicillin-resistant bacteria were determined using the broth microdilution method. The resistant strains were serotyped by the Public Health Institution. Epidemiologic relations of resistant strains were evaluated using ERIC-PCR. The presence of beta-lactamase genes and virulence factors were detected using PCR. RESULTS: The 117 S. enterica strains had ten isolates that were resistant to ampicillin, and the MIC range of ampicillin was found as 512-128 µg/mL. Ampicillin-resistant strains were susceptible to nalidixic acid, ciprofloxacin, cefotaxime, sulfamethoxazole/trimethoprim. Four different serotypes were identified and isolates were grouped into seven clusters. Five isolates carried blaTEM , and two carried the blaCTX-M gene. However, it was determined that blaSHV and blaPER genes did not exist in these strains. Virulence genes invA, pipD, and sopB were found in all isolates. sifA, pefA, and sopE genes were found in seven, four, and three isolates, respectively. CONCLUSION: Our data suggest that the rate of ampicillin resistance in S. enterica isolates was 8.5% in the two year period, but this ratio was generally lower than rates abroad. blaCTX-M and blaTEM genes could be responsible for ampicillin resistance. The blaSHV gene, which is highly prevalent in our country, was not found in any strains. sopB and pipD genes, which might be associated with beta-lactam resistance, were found in all strains. It is also noteworthy that the three isolates containing the sopE gene, which is associated with epidemic cases, were of the same serotypes and epidemiologic clusters.

Genotypic analysis of Escherichia coli strains that cause urosepsis in the Aegean region.

BACKGROUND/AIM: The aim of this study was to characterize strains genotypically, to determine their phylogenetic relationships, to investigate the presence of the papG gene, and to compare their antibiotic susceptibility test results. MATERIALS AND METHODS: Seventy pathogenic E. coli strains were isolated from both urine and blood cultures of patients with the preliminary diagnosis of urosepsis who were referred to the Ege University Faculty of Medicine, Bacteriology Laboratory of Medical Microbiology Department in Izmir. All of these strains were examined for the papG gene and phylogenetic groups with the multiplex polymerase chain reaction technique. Pulsed-field gel electrophoresis and multilocus sequence typing (MLST) were used for epidemiologic analysis. RESULTS: Phylogenetically, it was found that 16 belonged to group B2, 31 belonged to group D, 15 belonged to group A, and 7 belonged to group B1. One strain was not identified as belonging to a group. papG genes were found in 26 of 70 E. coli strains. Thirty urosepsis pathogenic E. coli strains were analyzed with MLST. Twenty-two strains were identified as new STs. CONCLUSION: These findings are extremely important for Turkey and these new 22 strains should be investigated in more detail because they are new and have the potential to lead to infections.

Investigation of enteropathogenic Escherichia coli and Shiga toxin-producingEscherichia coli associated with hemolytic uremic syndrome in Izmir Province, Turkey.

BACKGROUND/AIM: The purpose of this study was to investigate Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic Escherichia coli (EPEC) strains originating from diarrheagenic patients. MATERIALS AND METHODS: A total of 102 patients with diarrhea between October 2012 and January 2013 were enrolled in this study. Multiplex and standard polymerase chain reactions were performed to detect and distinguish STEC and EPEC strains. O serotyping of EPEC was carried out by monovalent antisera. The O and H serotyping of STEC strains was performed at the Refik Saydam Institute, Ankara. RESULTS: A total of 5 (3.42%) strains were identified as STEC, and 3 strains (2.05%) were atypical EPEC. One of the STEC serotypes was O157:H7 carrying VT1, Stx1A, and escv genes. The other STEC strain was identified as O174:H21, which is associated with hemolytic uremic syndrome and consists of VT2 and Stx2A genes. One of the EPEC and three of the STEC serotypes were nontypeable. The serotypes of the atypical EPEC strains were identified as O114 and O26. CONCLUSION: To the best of our knowledge, this is the first report of O174:H21 from the Izmir region that was shown to be a Shiga toxin-producing non-O157 serotype of STEC.