Department Of Clinical Microbiology Research Articles

A-290 Prevalence and Antimicrobial Resistance Pattern of Microorganisms Recovered From Bloodstream Infections From Public Hospitals of São Paulo City, Brazil

Abstract Background Nosocomial Bloodstream Infections (nBSI) are an important cause of morbidity and mortality. Brazilian studies concerning bloodstream infections are important tools that can bring specific issues related to antimicrobial resistance. The objective of this study was to describe the frequency and antimicrobial susceptibility profile of bacterial isolates from BSI in patients admitted to public hospitals in 2022 and 2023. Methods This study was a retrospective analysis from 12 hospitals (January 2022 to December 2023) based on BSI isolates laboratory data detected by the clinical microbiology department of a medical diagnostic laboratory. The identification and susceptibility tests were performed using MALDI-TOF mass spectrometry (Vitek MS) and Vitek®2 systems, according to the manufacture’s recommendations. Coagulase Negative Staphylococci (CoNS) BSI was only considered in the presence of at least two sets of positive blood cultures with the same organism. Results During the period (January 2022 to December 2023) a total of 19,588 microorganisms isolated from BSI were obtained from 12 hospitals. The frequency of organism group was Gram-positive (10,707; 54.7%), Gram-negative (7,874; 40.2%), yeasts (961; 4.9%) and filamentous (46; 0.2%). The order of prevalence (top ten) organisms was CoNS (5,149; 26.3%); Staphylococcus aureus (2,769; 14.1%); Klebsiella spp. (2,355; 12.0%); Escherichia coli (1,301; 6.6%); Acinetobacter spp. (1,293; 6.6%); Streptococcus spp. (1,125; 5.7%); Enterococcus spp. (1,112; 5.7%); Candida spp. (937; 4.8%); Pseudomonas spp. (749; 3.8%) and Proteus spp. (553; 2.8%). Extended spectrum beta-lactamase rates for E. coli and Klebsiella pneumoniae were 31.6% (268/848) and 74.9% (1027/1371), respectively. The resistance to carbapenems was detected mainly in 74.1% (661/892) of Acinetobacter spp. isolates, 60.7% (832/1371) of Klebsiella pneumoniae; 24.5% (114/465) of P. aeruginosa; 9.7% (34/349) of Proteus spp. and 1.4% (12/828) of Escherichia coli. Antimicrobial resistance was observed mainly in 87.2% of CoNS (2831/3247) and 44.5% of S. aureus (743/1669) to methicillin; 22.9% (146/637) of Enterococccus spp. to vancomycin. Conclusions The frequency of Klebsiella spp. isolates from nBSI has progressively increased and effective infection control measures should be taken to prevent them from spreading. The rates of antimicrobials resistance reported for Klebsiella pneumoniae, Acinetobacter spp., CoNS, S. aureus and Enterococcus spp. reinforce the high resistance rates to antimicrobials in São Paulo city.

Clinical and Radiological Features of Pyogenic and Brucellar Spondylodiscitis

Aim: Since spondylodiscitis continues to be seen with increasing incidence; thus, starting antibiotherapy targeted towards the etiological agent is crucial for reducing complications and mortality. This study aimed to determine the clinical and radiological characteristics of spondylodiscitis’ causative microorganisms. Material and Methods: Patients hospitalized in the Department of Infectious Diseases and Clinical Microbiology with a diagnosis of spondylodiscitis between 2015 and 2023 were retrospectively evaluated. Results: Low back pain was present in 97.5% of the total 40 patients as the most common symptom. Tissue biopsy culture results were obtained for 21 (52.5%) patients, with culture positivity observed in five (12.5%) patients. Consumption of raw milk/dairy products in the anamnesis and fever were found to be statistically significantly higher in patients with brucellosis (p < 0.001, p = 0.015), whereas neurological deficits were significantly higher in the pyogenic group (p = 0.007). No significant differences were observed between the pyogenic and brucella spondylodiscitis groups in terms of laboratory parameters (sedimentation rate, C-reactive protein, white blood cell count) and magnetic resonance imaging findings. Conclusion: Since no distinctive clinical and radiological parameters were identified for distinguishing between brucellar and pyogenic spondylodiscitis, serological tests for brucellosis should be investigated when considering the diagnosis, particularly in endemic regions. In cases of pyogenic spondylodiscitis, empirical antibiotic use prior to pathogen isolation may lead to delays in diagnosis and appropriate treatment, potentially resulting in complications such as neurological deficits. Therefore, interventional methods for tissue biopsy culture should be planned before antibiotherapy, especially in patients who do not immediately require antibiotherapy.

Genetic and phenotypic of Pseudomonas aeruginosa sensitive to meropenem antibiotics after exposure to meropenem.

Pseudomonas aeruginosa, drug-resistant, causes health infections. Resistance to the preferred therapy meropenem is a serious threat. This study aimed to analyze changes in meropenem minimum inhibitory concentration (MIC), changes in ampC, mexA, and oprD gene expression, and the correlation between MIC and ampC, mexA, and oprD gene expression after meropenem exposure. Ten isolates of P. aeruginosa from the Clinical Microbiology Department, Faculty of Medicine, Universitas Indonesia were used. After the bacteria were shown to be sensitive to meropenem phenotypically, intrinsic resistance genes were detected using PCR. After meropenem exposure on Days 5 and 12, sensitivity testing was carried out with the concentration gradient method and RNA was detected using real-time RT-PCR. All P. aeruginosa isolates that were phenotypically sensitive to meropenem had the ampC, mexA, and oprD genes. An increase in MIC, an increase in ampC and mexA gene expression, and a decrease in oprD gene expression were observed after meropenem exposure. There was a very strong and significant correlation (p ≤ 0.05) between MIC and oprD gene expression after Day 12 of meropenem exposure. Although there were no significant differences in MIC and ampC, mexA, and oprD gene expression between Day 5 and Day 12, there was a very strong and significant correlation between MIC and oprD gene expression on Day 12 (p ≤ 0.05). This indicates that decreasing oprD gene expression has the potential to increase meropenem resistance in Pseudomonas aeruginosa.

Impact of COVID-19 Restrictions on Incidence of Enteropathogenic Bacteria, Virus, and Parasites in Denmark: A National, Register-Based Study.

Diarrheal diseases caused by enteric pathogens are a significant public health concern. It is widely considered that close contact between persons, poor hygiene, and consumption of contaminated food are the primary causes of gastroenteritis. Clinical microbiology laboratory observations indicate that the incidence of enteropathogenic microorganisms may have been reduced in Denmark during the COVID-19 pandemic. All Departments of Clinical Microbiology in Denmark provided data on the monthly incidence of Salmonella spp., Escherichia coli, Campylobacter spp., Clostridioides difficile, Norovirus GI+GII, Giardia duodenalis, and Cryptosporidium from March 2018 to February 2021. The data were divided into three periods as follows: Control Period 1 (March 2018 to February 2019); Control Period 2 (March 2019 to February 2020); and the Restriction (pandemic) Period (March 2020 to February 2021). The incidences of pathogenic Salmonella spp.-, Escherichia coli-, and Campylobacter spp.-positive samples decreased by 57.3%, 48.1%, and 32.9%, respectively, during the restriction period. No decrease in C. difficile was observed. Norovirus GI+GII-positive samples decreased by 85.6%. Giardia duodenalis-positive samples decreased by 66.2%. Cryptosporidium species decreased by 59.6%. This study demonstrates a clear decrease in the incidence of enteropathogenic bacteria (except for C. difficile), viruses, and parasites during the SARS-CoV-2 restriction period in Denmark.

Microbial Pattern of Neonatal Sepsis in the Neonatal Intensive Care Unit of dr. Ramelan Navy Central Hospital.

The morbidity and mortality rates from neonatal sepsis remain high. However, there is limited information about the microbial pattern of neonatal sepsis in Indonesia. Microbial patterns can give an overview of the hygiene of an environment and act as a determinant for choosing definitive antibiotic treatment in neonatal sepsis patients. The organisms that cause neonatal sepsis differ from unit to unit and from time to time within the same unit. This study is aimed at discovering the microbial pattern of neonatal sepsis in the Neonatal Intensive Care Unit (NICU), dr. Ramelan Navy Central Hospital, in 2021-2022. This is a retrospective, cross-sectional study that takes secondary data from the NICU and clinical microbiology department of dr. Ramelan Navy Central Hospital. Data that met the inclusion and exclusion criteria available between January 1, 2021, and December 31, 2022, were collected. Patients whose blood cultures were positive for bacterial growth and diagnosed with sepsis were selected as the study sample. Out of 174 samples, 93 (53.4%) were found positive for bacterial infection and diagnosed as neonatal sepsis. Gram-negative isolates (96.8%) were predominant. Sixty-point-two percent of Klebsiella pneumoniae XDR, 19.4% of Klebsiella pneumoniae ESBL, and 8.6% of Burkholderia cepacia XDR were identified. The gram-positive isolates found in this study were only 3 samples (3.2%). Two-point-one percent of MRSA and 1.1% of Staphylococcus haemolyticus MDR were identified. The most common microorganisms causing neonatal sepsis in our NICU were gram-negative bacteria, particularly Klebsiella pneumoniae XDR. Following the recommended infection control procedures, practicing good hand hygiene, and having access to basic supplies and equipment are important to prevent and reduce the incidence of sepsis.

Bacteriological Study and Antibacterial Susceptibility in Ludwig’s Angina in a Tertiary Level Hospital in Dhaka, Bangladesh

Background: The knowledge of the local pattern of infection and antibacterial sensitivity in Ludwig’s angina is essential to enable efficacious treatment for it. Objective: To find out the pattern of bacteria responsible for developing Ludwig’s angina and their antibacterial susceptibility. Methods: It is a prospective, observational type of study carried out in the Department of Otolaryngology & Head-Neck Surgery, Dhaka Medical College Hospital, Dhaka, and the Department of Clinical Microbiology, ICDDR, B, Dhaka, Bangladesh, between April and September of 2016. A total of 100 patients were included in this study. Results: This study was done among 100 patients. In this study, 42 cases (42%) were in the 31-45 years age group. The male patients were 60 (60%) and females were 40 (40%). Majority of patients 70(70%) came from poor class family with educational level up to HSC (75%), maximum 35(35%) patients use meswak to clean teeth, 70 (70%) patients came from rural area, 70 (70%) patients had dental infection, 25 (25%) patients had diabetes mellitus, all the cases (100%) presented with swelling in the floor of the mouth and neck, pain and tenderness and fever. The major complication was necrotizing fasciitis 8 (8%), 36 (36%) patients were discharged within 1-2 weeks after treatment, Streptococcus 40 (40%) was the most common organism and the most effective antibiotic was Ceftriaxone (65%). Conclusion: The most frequently isolated organism in Ludwig’s angina is Streptococcus and sensitivity results showed a majority of isolates are susceptible to Ceftriaxone. Mugda Med Coll J. 2023; 6(2): 71-76

Comparison of the Distribution of Healthcare-Associated Infections and Causative Agents Between Intensive Care Units and Other Clinics.

To compare the trends in the distribution of healthcare associated infectious (HAIs) and causative agents in intensive care units (ICUs) and other clinics. Descriptive study. Place and Duration of the Study: Department of Infectious Diseases and Clinical Microbiology, Health Sciences University, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara, Turkiye, from 2015 to 2022. The study included patients who were diagnosed with HAIs and admitted to both the ICUs and the clinics. The data of HAIs identified between 2015-2022 were accessed and analysed retrospectively from the surveillance records of the IPC committee between 28.05.2023-07.08.2023. There was a decreasing trend observed in both ICU and clinics regarding the ratio of patients developing HAIs and the overall HAI rate (all p-values <0.001). These two measures were found to be significantly lower in the years 2019-2022 compared to the years 2015-2018. Over the years, particularly after 2020, a significant increasing trend in carbapenem resistance was observed in E. coli, K. pneumoniae, and P. aeruginosa (p=0.009, p<0.001, and p<0.001, respectively). The ratio of patients developing HAIs in the ICUs was higher than in the clinics (p<0.001). There was an increasing trend in the ratio of pneumonia and bloodstream infection (BSI) in ICUs. The increasing ratio of BSI and pneumonia in ICUs highlighted the need to review infection control bundles. Carbapenem resistance has been increasing over the years, suggesting that antimicrobial description and consumption practices should be re-evaluated, especially in the context of the COVID-19 pandemic. Intensive Care Unit, Healthcare-Associated Infections, Surveillance, Infection prevention and control, Antibiotic resistance.

Predicting the primary infection source of Escherichia coli bacteremia using virulence-associated genes

PurposeTo investigate the role of E. coli virulence-associated genes (VAGs) in predicting urinary tract infection (UTI) as the source of bacteremia in two distinct hospital populations, one with a large general catchment area and one dominated by referrals.MethodsE. coli bacteremias identified at Department of Clinical Microbiology (DCM), Hvidovre Hospital and DCM, Rigshospitalet in the Capital Region of Denmark from October to December 2018. Using whole genome sequencing (WGS), we identified 358 VAGs from 224 E. coli bacteremia. For predictive analysis, VAGs were paired with clinical source of UTI from local bacteremia databases.ResultsVAGs strongly predicting of UTI as primary infection source of bacteremia were primarily found within the pap gene family. papX (PPV 96%, sensitivity 54%) and papGII (PPV 93%, sensitivity 56%) were found highly predictive, but showed low sensitivities. The strength of VAG predictions of UTI as source varied significantly between the two hospital populations. VAGs had weaker predictions in the tertiary referral center (Rigshospitalet), a disparity likely stemming from differences in patient population and department specialization.ConclusionWGS data was used to predict the primary source of E. coli bacteremia and is an attempt on a new and different type of infection source identification. Genomic data showed potential to be utilized to predict the primary source of infection; however, discrepancy between the best performing profile of VAGs between acute care hospitals and tertiary hospitals makes it difficult to implement in clinical practice.

Comparison of clinician preference and HIV-ASSIST recommendations in antiretroviral therapy decision-making: A single center experience from Turkiye.

Background: HIV-ASSIST is a free, continuously updated, clinically validated online algorithm tool that synthesizes participant- and virus-specific characteristics and provides ART decision support based on the goals of maximizing viral suppression and tolerability. The aim of this study was to analyze the concordance of clinicians' ART preferences with HIV-ASSIST recommendations and the influencing factors. Methods: We conducted a cross-sectional retrospective cohort study using electronic medical records of people with HIV (PWH) followed in the Infectious Diseases and Clinical Microbiology Department of Health Sciences University Izmir Tepecik Training and Research Hospital. The concordance between prescribed ART and HIV-ASSIST recommendations was evaluated. Results: The study included 101 participants (92 male, 91.1%), median age was 35 (20-67), and 24.8% of participants were treatment-experienced. The concordance between prescribed ART and HIV-ASSIST recommendations was 90.1% (absolute concordance 60.4%). The concordance rate was 89.5% (absolute concordance rate was 64.5%) in treatment-naive participants; 92% (absolute concordance rate was 48%) in treatment-experienced participants. Factors that were associated with discordance in the multivariate analysis were co-trimoxazole prophylaxis and hyperlipidemia. Conclusion: The recommendations of the HIV-ASSIST algorithm were found to be highly concordant with the ART prescriptions of our clinicians.

Impact of a hospital sepsis management protocol on the selection of empirical antibiotics in infectious disease consultations

It is well-established that Infectious Diseases consultation (IDC) enhances the prognosis of bloodstream infections. However, it is unclear if adoption of an institutional sepsis protocol would lead to any further improvement in a setting where IDC and infectious diseases approval (IDA) - available throughout 7 days/24 hours -are mandatory for administering broad spectrum antibiotics. We aimed to evaluate the influence of the institutional sepsis protocol developed by Department of Infectious Diseases and Clinical Microbiology on the selection of appropriate empirical antibiotics by IDC through focusing on patients who had bloodstream infections caused by Extended-spectrum β-lactamase (ESBL) producing Escherichia coli and Klebsiella pneumoniae, which poses a therapeutic challenge. One hundred and fifty-three adult patients (58 patients in the pre-protocol period and 95 patients in the post-protocol period), who received empirical antibiotic treatment for ESBL-producing E. coli and K. pneumoniae, in whom at least one systemic antibiotic was started either on the day blood cultures were drawn or not later than 24 hours were included in the study, retrospectively. The primary outcome was whether the empirical treatment regimen included a carbapenem that was accepted as the appropriate treatment based on the results of the MERINO trial. Secondary outcomes included empirical treatment based on pre-defined risk factors suggesting multidrug resistance (MDR), 30-day inpatient mortality, and appropriate antibacterial treatment according to antimicrobial susceptibility test (AST) results. The median age (Interquartile range) was 61 (48-70.5) years and 76 (49.7%) out of 153 patients were male. The patients in the post-protocol period were older compared to the pre-protocol period (54 years vs 64 years, p = 0.045). The Charlson Comorbidity Index was higher during the post-protocol period compared to the pre-protocol period (4 vs 5, p=0.038). At least one risk factor for MDR bacteria infection was present in 147 (96.1%) of the 153 patients. While the rate of risk factors for MDR bacteria infections did not differ significantly between the pre-protocol and post-protocol periods, the post-protocol period showed a significantly higher level of appropriate antibiotic treatment according to the presence of MDR risk factors compared to the pre-protocol period (44.8% vs 64.2%, p=0.019). There was a significant increase in the use of carbapenems in the post-protocol period compared to the pre-protocol period (34.5% vs. 56.8%, p=0.007). When the subgroup of patients who were likely to have infection caused by ESBL-producing bacteria is taken into consideration, the carbapenem use was more frequent in the post-protocol period (37.8% vs 68.9%, p=0.002). The rate of appropriate empirical treatment according to AST was not statistically different between pre-protocol and post-protocol period. The 30-day mortality rates were similar in both periods (24.1% vs 31.5, p=0.33). However, the rate of susceptibility to piperacillin-tazobactam was statistically higher in the pre-protocol period (82.6% vs 46.2%, p=0.016) when 39.7% of the patients received piperacillin-tazobactam as the empirical treatment. This study highlights the significance of using a structured protocol to attain appropriate empirical treatment for patients suspected of sepsis, even in a setting where IDC is readily available.

A population-based study on the incidence and aetiology of infectious complications in peritoneal dialysis in South Sweden

Background Peritonitis is a major cause of morbidity in peritoneal dialysis (PD) and an independent risk factor for elevated all-cause mortality. The aims of this study were to report the incidence, trend, aetiology, and antimicrobial susceptibility of PD-associated peritonitis and catheter-related infections in South Sweden between 2011–2020. Methods This population-based observational cohort study included all patients with PD between the years 2011–2020 in the county of Skåne. Data was accessed through the Swedish Renal Registry and the Department of Clinical Microbiology in Lund. Definitions issued by the International Society for Peritoneal Dialysis were implemented to assess PD-associated infections. Results Medical records of 675 paediatric and adult PD patients were eligible for inclusion. Of those, 208 (31%) were female and the median age was 67 years (range 0-91). The overall rate of PD-peritonitis was 0.38 episodes per year at risk. Out of 484 episodes of peritonitis, 61% (n = 295) were caused by Gram-positive bacteria. There were 289 occurrences of exit site infections, of which most (n = 152, 53%) were Gram-positive. Tunnel infections occurred in 16 episodes and were caused by S. aureus or P. aeruginosa. Among all isolates, 37 were of MRSE, four of ESBL-producing E. coli, and one of MRSA. Conclusion The crude rate of PD-peritonitis was stable during the study period. Gram-positive bacteria dominated the microbial aetiology, and antibiotic resistance was limited. It is important to monitor the aetiology, incidence, and resistance rates in PD-associated infections, to base empirical antibiotic regimens and facilitate prevention.

Evaluation of Sysmex UF-5000 flow cytometer flag BACT-info for Gram discrimination in urinary tract infection

Urine culture as a gold standard for the diagnosis of urinary tract infection (UTI) involves a considerable workload in Clinical Microbiology Departments, due to the high number of samples received that will ultimately be negative. Therefore, it is necessary to use screening systems that also reduce the turnaround time for UTI diagnosis. The new flow cytometer UF-5000 (Sysmex Corporation) is able to differentiate between Gram-negative and Gram-positive bacteria using the BACT-info parameter according to manufacturer. The aim of our study was to evaluate the gram discrimination ability of the UF-5000 cytometer. A prospective study with 449 urine samples collected consecutively was conducted, in the period 7/3/2022-27/5/2022, in which the BACT-info flag was compared with urine culture as the reference method. The sensitivity obtained for both Gram-negative and Gram-positive bacteria was above 95%. However, for Gram-positive bacteria, the moderate Kappa index (0.49) and the low positive predictive value (37.1%) indicated that the correlation between BACT-info flag and urine culture was not acceptable and should not be reported to the requesting clinician. Implementation of the third generation UF-5000 cytometer represents a significant advance in the aetiological orientation of UTIs caused by Gram-negative bacteria. Reporting the Gram morphology in the urine samples reduces the response time in the microbiological diagnosis of UTI, which would have an impact on the reduction and optimisation of empirical treatment, and thus on the generation of antimicrobial resistance.

Presence of the blaTEM Gene in Commensal Neisseria spp.: A Possible Cause for the Acquired Drug Resistance Among Pathogenic Respiratory Bacteria.

Background The oral microbiome consists of various bacterial genera, withNeisseriaspp. being a prominent part of this niche. WhileNeisseria gonorrhoeaeandNeisseriameningitidisare human-restricted pathogens, non-pathogenicNeisseriaspecies likeNeisseria sicca,Neisseria perflava, etc.,are primarily commensals that can also behave as opportunistic pathogens. With increasing penicillin resistance in commensalNeisseria, there is a concern that these bacteria might harbor resistance genes that can be transferred to other pathogens. This study aimed to characterize the blaTEM gene (encodes for the plasmid-mediated β-lactamase enzyme that hydrolyzes the β-lactam ring) of commensalNeisseriaspp. isolated from respiratory samples. Methodology The research was conducted in the Department of Clinical Microbiology at Sri Ramachandra University, Chennai. The specimens used were sputum and throat swabs, which were subjected to a series of phenotypic methods and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) for speciation. The antibiogram was determined using the Kirby-Bauer disk diffusion method, and a PCR assay was utilized to identify theblaTEMgene responsible for β-lactamase production. Results Out of 274 processed samples, 65 unique commensalNeisseriaspp. were identified. The study highlighted the presence of theblaTEMgene in 93.9% (61) of the isolates, which is responsible for β-lactamase production. All isolates exhibitedresistance to penicillin. MostblaTEM-positive commensalNeisseria spp. were susceptible to cefuroxime (83.6%), ceftriaxone (85.2%), and cefotaxime (85.2%). The high prevalence of theblaTEMgene in commensalNeisseriais alarming. The gene, found on plasmids, could potentially transfer to other related species likeNeisseria gonorrhoeaeandNeisseriameningitidis, as well as other Gram-negative bacilli. Conclusion The presence of resistance genes in commensal bacteria is of concern, as they might be reservoirs for resistance transfer to pathogenic strains. The study emphasizes the importance of continuous monitoring and deeper investigations into commensal bacteria, emphasizing the need for a broader community screening approach to understand resistance mechanisms in the normal microbiome.

Bacterial profile and antimicrobial sensitivity pattern of blood specimen isolates in patients with bacteremia in the intensive care unit at Dr. Soetomo Hospital

Link of Video Abstract: https://youtu.be/2wcFE-82J2s Background: Critically ill patients in intensive care have a higher predisposition to acquire bacterial infections in the bloodstream. Research on bacterial profiles and blood culture sensitivity patterns in bacteremia patients can provide information for the basis of diagnosis, approaches, and treatment strategies in patients. To better understand the microbial profile and pattern of antimicrobial sensitivity of blood specimen isolate among non-COVID patients in the intensive care unit, we evaluated data from medical records that included blood cultures for all participants in the intensive care unit from January 2019 to April 2022. Method: A retrospective observational study with a cross-sectional approach was conducted in the Clinical Microbiology Department and Medical Record Unit at Dr. Soetomo Hospital. Data on surgical and non-surgical noncovid patients with bacteremia in intensive care unit patients was collected from January 2019 to April 2022. The Sample was taken with a consecutive sampling technique. Results: There were 140 isolates with positive blood culture results. The most common bacteria are coagulase-negative Staphylococcus 22 (15.7%), Acinetobacter baumanii 25 (17.9%), and Pseudomonas aeruginosa 13 (4.9%) in surgical and non-surgical patients. Sensitivity to Gram-positive bacteria in surgical and non-surgical patients before the pandemic linezolid 75% and vancomycin 58,3%. During pandemic linezolid at 76.9% and vancomycin at 69.2%. Sensitivity of Gram-negative bacteria in surgical patients before the pandemic was imipenem 57.1%, meropenem 57.1%, and amikacin 47.6%. During the pandemic, amikacin 73.5%, meropenem 55.1%, and imipenem 53.1%. Non-surgical patients before the pandemic gram negative sensitivity to meropenem was 100%, ceftazidime 66.7%. During the pandemic, amikacin 59.1%, and cotrimoxazole 45.5%. Conclusion: There was no difference in the surgical and non-surgical bacterial profiles before the pandemic and during the pandemic.

Etiological factors of bloodstream infections in oncological patients, who was hospitalized at the National Institute of Maria Skłodowska-Curie - National Research Institute in Warsaw in 2020-2022.

The purpose of the study was the microbiological analysis of bloodstream infections in patients hospitalized at the National Institute of Oncology, Maria Skłodowska-Curie - National Research Institute in the period from 01/01/2020 to 31/10/2022. In the period from 01/01/2020 to 31/10/2022, 18,420 blood cultures obtained from patients hospitalized at the NIO-PIB were analysed in the Department of Clinical Microbiology (total for the presence of bacteria and fungi). Culture for the presence of bacteria was carried out in the BactAlert automatic system by bioMerieux, and for fungi in the Bactec FX automatic system by Becton Dickinson. 1,184 strains of bacteria and 32 strains of fungi considered to be the etiological factor of the infection were cultured from clinical samples. Gram-positive bacteria accounted for 61.57%, while Gram-negative bacteria accounted for 32.26% of all isolated bacterial strains. The most frequently cultured strains were Escherichia coli - 13.77% (including 22.1% of ESBL strains), Klebsiella penumoniae - 4.6% (44.4% of ESBL strains, 1.85% of NDM strains), Enterobacter cloacae - 2 .7% (including 40.6% of multi-resistant strains: ESBL (15.6%) or with AmpC derepression (25%), among the non-fermenting bacilli, Pseudomonas aeruginosa was the most frequently cultured - 4.18% (including 3.8% MBL) and Acinetobacter baumannii - 0.8% (including CRAB strains 50%, MBL 10%). Anaerobic microorganisms were responsible for 3.46% of blood infection cases. Yeast- like fungi were a factor in 2.7% of all fungemia cases. From blood samples taken Staphylococci were more frequently isolated directly from a vein or through a central venous catheter than aerobic Gram-negative bacilli (44.7% and 25.3% and 55.6% and 12.5%, respectively). The opposite situation occurred in the case of samples taken simultaneously directly from vein and through a central venous catheter, in which a higher share of aerobic Gram-negative bacilli (46.6%) than staphylococci (32.8%) in causing blood infections was observed. Gram-positive bacteria are the major contributors to bloodstream infections in cancer patients. There is a growing tendency to develop BSI caused by multi-resistant strains.

Antibiogram of Acinetobacter baumannii isolated from Intensive Care Unit at Prof. dr. I.G.N.G. Ngoerah Hospital in 2020-2022

Background: Acinetobacter baumannii infection is a severe problem since it tends to be multi-resistant to many antibiotics. This study aimed to determine the prevalence of A. baumannii isolated from blood, urine, and sputum cultures and their antibiotic resistance patterns. Methods: Data of A. baumanii isolated from clinical specimens of Intensive Care Unit (ICU) wards patients were collected retrospectively from laboratory records in the Clinical Microbiology Department of Prof. Dr. I. G. N. G. Ngoerah General Hospital during 2020-2022. Identification and antimicrobial susceptibility tests were conducted using the Vitek-2 Compact system (bioMérieux, France). Isolates resistant to ≥ 3 antibiotic classes were categorized as multidrug-resistant (MDR) A. baumanii. Results: A. baumanii collected from sputum, blood, and urine in Intensive Care Unit (ICU) wards were 63%, 13%, and 7.5% from 2020 until 2022. Most A. baumanii isolates in 2020, 2021, and 2022 were susceptible to Amikacin, which was 75%, 78%, and 76%, respectively. Furthermore, the isolates that were susceptible to Trimethoprim/Sulfamethoxazole were 66%, 81%, and 72%, followed by Tigecycline, 80%, 61%, and 56% respectively. A. baumanii, however, showed low sensitivity to Meropenem even though susceptibility is getting higher each year. Almost all the isolates were resistant to ceftriaxone. Conclusions: Acinetobacter baumannii isolates isolated during 2020-2022 showed high resistance to penicillin, cephalosporin and fluoroquinolones. Although A. baumanii was resistant to carbapenem, its susceptibility tends to increase throughout the 3 years of this study. These data could be considered for empirical therapy of A. baumanii infections.

Exploring the dynamics of Borrelia burgdorferi sensu lato antibodies—a registry-based study on laboratory data from Sweden and Denmark

ObjectivesLyme borreliosis (LB) is the most common tick-transmitted infection in the northern hemisphere and is caused by bacteria in the Borrelia burgdorferi sensu lato (Bbsl)-complex. The diagnosis is partially based on serology, and clinicians often take follow-up serum samples to look for seroconversion or an increase in IgG-antibody levels. In this registry-based study, we proposed a method for determining actual changes in IgG and examined antibody reactivity and decay. MethodsSerological data from the departments of clinical microbiology at Karlstad Hospital, Sweden, and Slagelse Hospital, Denmark, were used to calculate a seroreactivity cut-off (SCOFF), above which changes between two samples from the patient cannot be explained by random variation. Increases in IgG reactivity as well as IgG and IgM decay were illustrated using time-to-event analysis and the SCOFF. ResultsA total of 44,861 serum samples from 34,157 patients were tested for Bbsl-antibodies. Of the 4301 patients with follow-up samples taken within 100 days, 201 (4.67%) were above the SCOFF of 1.42 with a median time to follow-up sample of 36 days (interquartile range: 21). IgG demonstrated longer median time for all antibody levels (indeterminate: 4.6 years, low: 7.0 years, moderate-high: 8.8 years) than IgM antibodies (indeterminate: 2.1 years, low: 3.9 years, moderate-high: 6.8 years) and higher initial antibody levels persisted significantly longer for both IgG and IgM antibodies (p < 0.001). Of the 7868 patients with follow-up samples, isolated IgM reactivity preceded an increase in IgG reactivity in 18 patients (0.23%). DiscussionThe SCOFF indicated little biological and random variation for Bbsl-specific IgG antibodies on the platforms used during the study. In most follow-up samples, both IgG and IgM antibodies persisted for years, with longer seropositivity associated with high initial antibody levels and IgG-type antibodies. The diagnostic value of isolated IgM reactivity was limited.

COMPARISON OF CLINICAL, LABORATORY FINDINGS AND COMPLICATIONS IN BACTERIEMIC AND NONBACTERIEMIC BRUCELLOSIS: A SINGLE CENTER EXPERIENCE

Objective: Brucellosis is a systemic zoonosis that affects various organs or body systems and can mimic many diseases. Symptoms can range from acute febrile illness to chronic clinical manifestations with severe complications. In our study, we investigated the relationship between bacteremia and clinical and laboratory findings, and complications in patients with brucellosis.&#x0D; Material and Methods: Two hundred and twenty-three patients diagnosed with brucellosis between 2005 and 2020 in the department of infectious diseases and clinical microbiology of a tertiary care university hospital were included in the study. Rose Bengal test, Brucella standard tube agglutination test and culture (blood and/or bone marrow culture) were used for the diagnosis of brucellosis. The patients were divided into two groups according to their bacteremia status. Patients with positive culture were identified as bacteremia, and patients with negative culture were identified as non-bacteriemic.&#x0D; &#x0D; Results: A total of 223 patients were included in the study, of which 142 (63.7%) were male. While weight loss, fever and hematological complications were higher in bacteremia cases (p=0.001, p

Increased demand of urine cultures from Danish general practice: a five-year register-based study

Objective To characterise and explore the development in the number and content of urine samples sent from general practice in the North Denmark Region to the Department of Clinical Microbiology (DCM) at Aalborg University Hospital during a five-year period. Design A register-based study. Setting General practice. Subjects Urine samples received at DCM, Aalborg University Hospital from general practice between 2017 and 2022. Main outcome measures Number and content of urine samples. Results A total of 255,271 urine samples from general practice were received at DCM, with 76.1% being from female patients. Uropathogens were identified in 43.0% of the samples. During the five-year period, a 23.0% increase in the number of urine samples per person (incidence rate ratio (IRR) 1.23, 95% CI 1.21–1.25) was observed. A slight increase in the proportion of positive cultures (risk ratio (RR) 1.03, 95% CI 1.01–1.05) was seen. No notable change in the patient population (age, gender) was observed. Overall, Escherichia coli was the most identified uropathogen (60.4%) followed by Klebsiella spp. (8.7%) and Enterococcus spp. (7.7%). Distribution of the various uropathogens differed slightly depending on patient gender and age, importantly E. coli was less frequently observed in males aged >65 years. Conclusion During the past five years an increasing amount of urine cultures have been requested at DCM from general practice. Importantly, the cause(s) of this increasing demand needs to be explored further in future studies.

Borderline SARS-CoV-2 patients: the trace behind

ABSTRACT Background Effective and precise SARS-CoV-2 detection assays are crucial for maintaining regular hospital routines and identifying infected hospital employees and infected patients before hospital admission. Inconclusive PCR test results of potentially infectious borderline SARS-CoV-2 patients can confuse clinicians and delay appropriate infection control. Objectives and study design In this retrospective study, we followed up borderline SARS-CoV-2 patients who were tested (from the second sample with the same method) at the Clinical Department of Clinical Microbiology. We aimed to determine the positivity conversion ratio within 7 days after inconclusive PCR test results. Results Out of 247 borderline patients, who were resampled and retested in the same laboratory, 60 patients (29.4%) showed conversion of the borderline viral load (inconclusive RT-PCR test) to a positive RT-PCR test result. Conclusions Our results highlight the need for retesting of borderline patients with inconclusive SARS-CoV-2 results. Follow-up testing of inconclusive PCR results within 7 days can identify additional positive results and reduce the potential risk of intrahospital transmission.