Surveillance of respiratory viruses by aerosol screening in indoor air as an early warning system for epidemics.

The development of effective methods for the surveillance of seasonal respiratory viruses is required for the timely management of outbreaks. We aimed to survey Influenza-A, Influenza-B, RSV-A, Rhinovirus and SARS-CoV-2 surveillance in a tertiary hospital and a campus over 5 months. The effectiveness of air screening as an early warning system for respiratory viruses was evaluated in correlation with respiratory tract panel test results. The overall viral positivity was higher on the campus than in the hospital (55.0% vs. 38.0%). Influenza A was the most prevalent pathogen in both locations. There were two influenza peaks (42nd and 49th weeks) in the hospital air, and a delayed peak was detected on campus in the 1st-week of January. Panel tests indicated a high rate of Influenza A in late December. RSV-A-positivity was higher on the campus than the hospital (21.6% vs. 7.4%). Moreover, we detected two RSV-A peaks in the campus air (48th and 51st weeks) but only one peak in the hospital and panel tests (week 49). Although rhinovirus was the most common pathogen in panel tests, rhinovirus positivity was low in air samples. The air screening for Influenza-B and SARS-Cov-2 revealed comparable positivity rates with panel tests. Air screening can be integrated into surveillance programs to support infection control programs for potential epidemics of respiratory virus infections except for rhinoviruses.

A novel rapid bioluminescence-based antimicrobial susceptibility testing method based on adenosine triphosphate consumption.

Introduction: Standard, phenotypic antimicrobial susceptibility testing (AST) methods require 16-20 h of incubation and are considered as the bottleneck in providing timely input for appropriate antimicrobial treatment. In this study, a novel adenosine triphosphate (ATP)-bioluminescence-based method which allows rapid AST within 3 h was described. Methods: Standard AST was performed for 56 Enterobacterales isolates using EUCAST disk diffusion (DD) methodology. For the bioluminescence-based rapid AST, suspensions of bacteria were prepared using Mueller-Hinton broth to obtain a turbidity of 0.5 McFarland. The suspensions were distributed into 96-well microtiter plates. ATP (20 mM) and fixed concentrations of different antibiotics were added. Following incubation at 37°C for 1 h, a luminescent reaction mixture, including the substrate luciferin and luciferase enzyme solutions, was added. The chemiluminescence was monitored using an imaging system. Light production demonstrated the presence of ATP, indicating that the isolate was susceptible to the antibiotic in the well. Absence or decrease of light intensity, compared with the growth control well, indicated the use of ATP as an indirect measure of bacterial growth, and therefore resistance to the antibiotic in the well. Results: The novel AST method was tested using a total of 348 test wells. Concordance was achieved for 290 (83.3%) of the tests, whereas 52 (14.9%) and 6 (1.7%) tests caused minor and major errors, respectively. Discussion: In this study, a bioluminescence-based rapid AST was developed based on the consumption of ATP by bacteria. Our method's uniqueness relies on determining ATP consumption by microorganisms in the presence or absence of an antibiotic. The novel AST method described in this study lays the groundwork for obtaining rapid results, which should be considered as a proof of concept. With further optimization studies, this novel method can provide higher accuracy and be introduced into clinical practice as a routine AST method.

Pseudomonasaeruginosa antimicrobial susceptibility profiles, resistance mechanisms and international clonal lineages: update from ESGARS-ESCMID/ISARPAE Group.

SCOPE: Pseudomonas aeruginosa, a ubiquitous opportunistic pathogen considered one of the paradigms of antimicrobial resistance, is among the main causes of hospital-acquired and chronic infections associated with significant morbidity and mortality. This growing threat results from the extraordinary capacity of P. aeruginosa to develop antimicrobial resistance through chromosomal mutations, the increasing prevalence of transferable resistance determinants (such as the carbapenemases and the extended-spectrum ß-lactamases), and the global expansion of epidemic lineages. The general objective of this initiative is to provide a comprehensive update of P. aeruginosa resistance mechanisms, especially for the extensively drug-resistant (XDR)/difficult-to-treat resistance (DTR) international high-risk epidemic lineages, and how the recently approved ß-lactams and ß-lactam/ß-lactamase inhibitor combinations may affect resistance mechanisms and the definition of susceptibility profiles. METHODS: To address this challenge, the European Study Group for Antimicrobial Resistance Surveillance (ESGARS) from the European Society of Clinical Microbiology and Infectious Diseases launched the 'Improving Surveillance of Antibiotic-Resistant Pseudomonas aeruginosa in Europe (ISARPAE)' initiative in 2022, supported by the Joint programming initiative on antimicrobial resistance network call and included a panel of over 40 researchers from 18 European Countries. Thus, a ESGARS-ISARPAE position paper was designed and the final version agreed after four rounds of revision and discussion by all panel members. QUESTIONS ADDRESSED IN THE POSITION PAPER: To provide an update on (a) the emerging resistance mechanisms to classical and novel anti-pseudomonal agents, with a particular focus on ß-lactams, (b) the susceptibility profiles associated with the most relevant ß-lactam resistance mechanisms, (c) the impact of the novel agents and resistance mechanisms on the definitions of resistance profiles, and (d) the globally expanding XDR/DTR high-risk lineages and their association with transferable resistance mechanisms. IMPLICATION: The evidence presented herein can be used for coordinated epidemiological surveillance and decision making at the European and global level.

COVID-19 associated bacterial infections in intensive care unit: a case control study.

We described the secondary bacterial infections (SBI) among COVID-19 patients in comparison with non-COVID-19 patients. We performed a retrospective case-control study between January 01, 2020 and April 01, 2022. Including the adult patients, who stayed ≥ 72 h in intensive care unit (ICU). In total 405 patients were included, 135 had (33.3%) COVID-19, with similar age and gender. The length of stay in ICU was not different (11.4 vs 8.2, p = 0.109), however mean intubation days were higher among COVID-19 cases (6.5 vs 3.8, p = 0.005), SBI were more common among COVID-19 cases (34% vs 10.7%, p < 0.001). Among the patients with pneumonia, the rate of gram-positive bacteria was higher in COVID-19 group than the control group (39% vs 5%, p = 0.006). The predictors for SBI were having COVID-19 (OR: 2.3, Cl 1.25-4.32, p = 0.008), days of intubation (OR: 1.05, Cl 1.01-1.10, p = 0.004), and being male (OR: 2, Cl 1.12-3.58, p = 0.018). The predictors of mortality were COVID-19 (OR: 2.38, Cl 1.28-4.42, p = 0.006), days of intubation (OR: 1.06, Cl 1.03-1.09, p < 0.001), active hematologic malignancy (OR: 3.1, Cl: 1.33-7.28, p = 0.09), active solid tumors (OR: 2.44, Cl 1.21-4.91, p = 0.012), and coronary artery diseases (OR: 1.8, Cl 1.01-3.52, p = 0.045). The most common SBI in COVID-19 patients were methicillin-sensitive Staphylococcus aureus. No carbapenem-resistant Enterobacterales related infections were detected in COVID-19 patients.

Duration of infectious shedding of SARS-CoV-2 Omicron variant and its relation with symptoms.

OBJECTIVES: SARS-CoV-2 infections with Omicron variants have a high capability of human-to-human transmission. Nevertheless, the duration of isolation for mild cases was shortened to 5 to 7 days. We aimed to detect the duration of viral shedding among healthcare workers (HCWs) with Omicron by using viral culture. METHODS: We prospectively included newly diagnosed nonsevere, symptomatic SARS-CoV-2 positive HCWs. Nasopharyngeal swab samples were obtained consecutively on days 5, 7,10, and 14 of onset of symptoms. The samples were examined by nucleic acid amplification test and viral culture. RESULTS: In total, 55 non-severe patients with SARS-CoV-2 Omicron variant were included. The mean age of the population was 34 years (range, 23 to 54) and 78% (43/55) were female. The PCR positivity rate on days 5, 7, 10, and 14 was 96.4% (53/55), 87.3% (48/55), 74.545% (41/55), and 41.8% (23/55) consecutively, whereas the viral culture positivity rates were 83% (44/53), 52% (26/50), 13.5% (7/52), and 8% (4/50). Among the patients who became symptom-free, the viral culture positivity rates were 100% (4/4), 58% (7/12), 11% (3/27), and 5% (2/41). DISCUSSION: We showed that among the SARS-CoV-2 Omicron variant infected patients, viral shedding continues for ≥10 days in 13.5% of all cases and 11% in symptom-free cases. The decision for cessation of isolation according to the presence of symptoms could be reconsidered until further studies disapprove of our results. Meanwhile, the infected HCWs who give care to high-risk patients for severe COVID-19 might extend their isolations ≤10 days after the onset of symptoms, regardless of their symptoms.

[The Use of Resapolymyxin NP Test in Determining the Sensitivity of Colistin in Escherichia coli, and Klebsiella pneumoniae Isolates]. / Escherichia coli ve Klebsiella pneumoniae Izolatlarinda Kolistin Duyarliliginin Belirlenmesinde ResaPolymyxin NP Testinin Kullanimi.

Colistin is used as the last choice of drug in multidrug resistant gram-negative bacilli infections; therefore, accurate detection of colistin susceptibility has gained critical importance. Unfortunately, many of the widely used and practical methods in the clinical laboratory have various limitations for the determination of colistin susceptibility. This situation has led researchers to search for new methods to determine colistin susceptibility. In this study, the performance of the ResaPolymyxin NP test, which was developed for the rapid detection of colistin susceptibility of Pseudomonas aeruginosa and Acinetobacter baumannii isolates, was evaluated for various Gram-negative bacteria for the determination of colistin susceptibility. For this purpose, the colistin MIC values of 105 Escherichia coli, and 196 Klebsiella pneumoniae isolates were determined by broth microdilution (BMD) using cation-adjusted Mueller-Hinton broth and then ResaPolymyxin NP test was applied for each isolate. While 242 (%80.4) of the isolates included in the study were found to be susceptible to colistin with BMD, 214 (71.1%) of the isolates were found as sensitive to colistin with the ResaPolymyxin NP test. The categorical agreement rate for the ResaPolymyxin NP test was 85.7% for E.coli isolates, and 92.3% for K.pneumoniae isolates. The major error rate was 14.7% for E.coli, 10.8% for K.pneumoniae, whereas the very major error rate was 1.8% for K.pneumoniae. For ResaPolymyxin NP test, sensitivity, specificity, positive and negative predictive values were %98,3; %88.0; %66.7; and %99.5. In contrast to the available data about the ResaPolymyxin NP test, both the categorical agreement rate with BMD, and the very major and major error rates varied according to the isolate type, and it was concluded that the test performed relatively better in E.coli and K.pneumoniae isolates. Since the data obtained in this study are quite different from the previously published data, more comprehensive and multicenter studies are needed to evaluate the test effectiveness in order to recommend the use of the ResaPolymyxin NP test in clinical microbiology laboratories.

Placental deficiency during maternal SARS-CoV-2 infection.

INTRODUCTION: Maternal anti-SARS-CoV-2 Spike antibodies can cross the placenta during pregnancy, and neonates born to infected mothers have acquired antibodies at birth. Few studies reported data on the histopathological changes of the placenta during infection and placental infection. SARS-CoV-2 infection may cause impaired development of the placenta, thus predisposing maternal and fetal unfavorable outcomes. The prospective study aims to evaluate the risk of vertical transmission of SARS-CoV-2 and placental passage of anti-Spike antibodies as well as the impact of clinical severity on placental structures. METHODS: This is a prospective cohort study on 30 pregnant women infected by SARS-CoV-2 with their neonates. The demographic features and pregnancy outcomes were collected. Gross and microscopic examinations of the placentas were done. Maternal and umbilical cord sera were obtained at the time of delivery. Nasopharyngeal swabs were collected from neonates immediately after birth. RESULTS: The concentrations of total anti-SARS-CoV-2 Spike antibodies were higher in pregnant women with moderate to severe/critical disease. The maternal total anti-SARS-CoV-2 Spike levels were correlated with those of neonatal levels. The rate of placental abnormalities is high in the mothers with severe disease, and those with positive anti-SARS-CoV-2 IgM. All neonates had negative nasopharyngeal swabs for SARS- CoV-2 infections and all placentas were negative in immunohistochemical staining for Spike protein. DISCUSSION: The maternally derived anti-SARS-CoV-2 Spike antibody can transmit to neonates born to infected mothers regardless of gestational age. Our results indicated that the disease severity is associated with ischemic placental pathology which may result in adverse pregnancy outcomes.

Gardnerella vaginalis: Is it an Underestimated Cause of Urinary Symptoms in Males?

Objective: This study aimed to investigate the detection rate of Gardnerella vaginalis by multiplex PCR test in the genitourinary samples of male patients with suspected urethritis and related symptoms. Materials and Methods: A total of 144 male patients who presented to our department between February 2021 and October 2021, either with urinary symptoms or concerns following unprotected sex, were included in the study.A total of 128 (88.9%) first-void urine samples, 15 (10.4%) urethral swabs, and one (0.7%) semen sample were obtained. NeoPlex STI-14 Detection Multiplex PCR Kit (GeneMatrix Inc. Seongnam, South Korea) was used to investigate any of the following pathogens: Candida albicans, Chlamydia trachomatis, G. vaginalis, Mycoplasma genitalium, Mycoplasma hominis, Neisseria gonorrhoeae, Trichomonas vaginalis, Ureaplasma parvum, Ureaplasma urealyticum,herpes simplex virus type 1 (HSV-1), herpes simplex virus type 2 (HSV-2), Treponema pallidum , Streptococcus agalactiae, and Haemophilus ducreyi. The patients with positive results for G. vaginalis were retrospectively analyzed. Results: The patients' median age was 37 (range: 21 to 71 years old). G. vaginalis was the most frequently detected microorganism (n=23; 15.9%). Other microorganisms found in order of frequency were U. urealyticum (n=19; 13.2%), U. parvum (n=15; 10.4%), C. trachomatis (n=11; 7.6%), M. genitalium (n=8; 5.6%), HSV-2 (n= 7; 4.9%), N. gonorrhoeae (n=6; 4.2), HSV-1 (n=2; 1.4%), M. hominis (n=1, 0.7%), and C. albicans (n=1, 0.7%). Fifteen patients (65%) were positive for one or two microbial agents together with G. vaginalis, while in eight patients (35%), G. vaginalis was the only isolated agent. Six of these eight patients and 14 of the remaining 15 were symptomatic. Conclusion: With the introduction of multiplex PCR tests, including those for G. vaginalis, we can expect a higher detection rate of these species of bacteria in male genitourinary samples, which could be the cause of unexplained urinary/urethral symptoms.

The Investigation of Malaria Cases in a Central Laboratory in Istanbul Region for a Period of Fifteen Years

Objective: The aim of this study is to examine the cases with malaria identified in the last 15 years in a central laboratory in Istanbul and assess their clinical features in general. Methods: A retrospective examination of the laboratory records of all malaria-suspected patients whose thin and thick smears of blood samples were examined between 2002 and 2017 was conducted. Cases diagnosed as having malaria were evaluated in terms of their personal features such as age and gender, complaints and findings at the time of diagnosis, clinical features and recent travel history to an endemic region. Results: Blood smears of 2271 patients were examined and Plasmodium spp. were detected in a total of 42 cases during the abovementioned period. Among these 42 cases, Plasmodium falciparum was detected in 19, Plasmodium ovale in 1 and Plasmodium vivax in 22 cases. It was noted that 32 of 42 cases were diagnosed in the last five years, and were infected during journey to Africa. July was found to be the month with highest number of cases. Conclusion: Almost all cases with malaria were imported cases due to P. vivax or P. falciparum, as expected. It is remarkable that, the demand for blood smear examinations due to the suspicion of malaria by physicians has increased and the number of cases with malaria detected in the laboratory has increased too, in recent years.

Evaluation of the performance of MALDI-TOF MS and DNA sequence analysis in the identification of mycobacteria species

Background/aim: Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry is an alternative way of identifying mycobacteria via the analysis of biomolecules. It is being increasingly used in routine microbiology practice since it permits early, rapid, and cost-effective identification of pathogens of clinical importance. In this study, we aimed to evaluate the efficacy of phenotypic identification of mycobacteria by the MALDI-TOF MS MBT Mycobacteria Library (ML) 4.0 (Bruker, Daltonics) compared to standard sequence analysis. Materials and methods: A total of 155 Mycobacterium clinical and external quality control isolates, comprising nontuberculous mycobacteria (NTM) (n = 95) and the Mycobacterium tuberculosis complex (MTC) (n = 60), were included in the study. Results: Identification by MBT ML4.0 was correctly performed in 100% of MTC and in 91% of NTM isolates. All of the MTC isolates were correctly differentiated from NTM isolates. Conclusion: Based on our results, MBT ML4.0 may be used reliably to identify both NTM and MTC.

Evaluation of the Carba NP Test for the Detection of Carbapenemase Activity in Bacteroides Species.

We evaluated the usefulness of the Carba NP test for rapid detection of carbapenemase activity in Bacteroides spp. The minimum inhibitory concentration (MIC) for imipenem was determined with gradient test strips, and cfiA gene was investigated by polymerase chain reaction for 27 clinical Bacteroides spp. isolates. Carba NP test was performed according to recommendations of the Clinical and Laboratory Standards Institute. Among three cfiA gene harboring clinical isolates, two imipenem resistant isolates were Carba NP test positive, while the imipenem intermediate isolate was negative. Our preliminary results suggest that the Carba NP test can be useful as a rapid test to detect carbapenemases in Bacteroides species.

[Molecular epidemiology, antimicrobial resistance and characterization of extended-spectrum beta-lactamases of Salmonella enterica serotype Paratyphi B clinical isolates]. / Salmonella enterica serotip Paratyphi B klinik izolatlarinin moleküler epidemiyolojisi, antimikrobiyal direnci ve genislemis spektrumlu beta-laktamazlarinin karakterizasyonu.

Although Salmonella enterica serotype Paratyphi B is the less frequently isolated serotype worldwide and in Turkey, it is the most common serotype in our hospital, with a marked increase in 2007. The purpose of this study was to investigate the antibiotic susceptibility and the extended spectrum beta-lactamase (ESBL) profile, and molecular epidemiology of S. Paratyphi B isolates detected in our hospital microbiology laboratory. Seventy isolates identified as S. Paratyphi B from 109 Salmonella isolates obtained from clinical specimens from different patients between October 2005 and December 2012, were included in the study. In addition to conventional methods, isolates were identified using the Phoenix automated microbiology system (Becton Dickinson, USA). Serotyping of the isolates was performed on the basis of slide agglutination and the Kauffmann-White scheme. The antibiotic susceptibility of the isolates was determined using the BD Phoenix' automated system and disk diffusion test. ESBL enzymes were investigated using the combined disk test, isoelectric focusing, polymerase chain reaction (PCR) and sequence analysis. The molecular epidemiology of the 51 isolates obtained between October 2005 and August 2008 was examined with pulsed-field gel electrophoresis (PFGE) using the XbaI enzyme. S. Paratyphi B isolates were obtained from 70 specimens (46 blood, 16 fecal, 4 bone marrow, 2 urine and 2 wound) each from different patients. Resistance to nalidixic acid was determined in 18.6%, resistance to ampicillin, cefotaxime and cefepime in 2.9% and to ceftazidime and co-trimoxazole in 1.4% of the isolates. ESBL production was detected only in two isolates; in one TEM-1 was accompanied by CTX-M-15 and in the other isolate CTX-M-3 was found. Forty-six of the 51 isolates (90%) were found to be genetically related by PFGE and were placed in cluster A. The distribution of the isolates in cluster A revealed six subtypes as A1 (n= 7), A2 (n= 11), A3 (n= 7), A4 (n= 18), A5 (n= 2) and A6 (n= 1). Three different patterns not related to the cluster A were determined in the remaining five isolates (two were B, one of each was C, D and E). In conclusion, although the rate of antibiotic resistance was low in the S. Paratyphi B isolates in our hospital, rare types of ESBLs such as CTX-M-3 and CTX-M-15 were detected in Salmonellae. As far as the current literature is considered, this is the first report in Turkey of blaCTX-M-15 in Salmonella spp. and blaCTX-M-3 genes in S. Paratyphi B. The results may indicate a possible future threat to the treatment of Salmonella infections. Since most of the isolates were genetically related, this might suggest an epidemic in our region.