Department Of Clinical Microbiology Research Articles

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.

Why Product Information Should not be Set in Stone: Lessons from a Decade of Linezolid Therapeutic Drug Monitoring: An Opinion Paper.

*Department of Clinical Microbiology and Infectious Diseases, St Vincent's Hospital, Sydney, Australia; and †Unit of Clinical Pharmacology, ASST Fatebenefratelli Sacco University Hospital, Milan, Italy. Correspondence: Deborah J. E Marriott, MD, Department of Clinical Microbiology and Infectious Diseases, St Vincent's Hospital, Sydney, NSW 2068, Australia (e-mail: [email protected]). Conflicts of Interest and Source of Funding: None declared

Bruselloz; Endemik Bölgelerde Tanı Zorluğu

Introduction: Brucellosis is a zoonotic disease distributed worldwide and very important public health problem especially in the developing countries. In this study, we aimed to evaluate the clinical/laboratory findings of brucellosis patients and contribute of coombs testing to diagnosis at Iğdır State Hospital infection diseases and clinical microbiology department. Materials and Methods: One hundred and forty-five brucellosis patients followed up in our clinic between September 2012 and February 2013 were evaluated retrospectively. Demographic characteristics, laboratory findings, diagnostic methods of the patients were presented. Results: The mean age of the patients were 39±15 (18-80) and 59% (n=86) of the patients were female, 41% (n=59) were male. Most frequent risk factors were animal breeding (n=115, 79%) and using underdone milk and milk products (n=98, 69%). Most reported complaints were weakness (92%), arthralgia (89%), sweating (74%), lack of appetite (70%) and fever (68%). Fifty-seven of the brucellosis patients could not diagnosed with standard tube agglutination. Therefore, Coombs test was used for these undiagnosed patients (39%, n=57). Eighty patients were evaluated as acute (55%), 53 as subacute (37%) and 12 as chronic (8%) brucellosis. Conclusions: Brucellosis can affect all organ systems and cause different clinical manifestations. Therefore, difficulties are encountered in the diagnosis of the disease. Brucellosis should be kept in mind in the differential diagnosis especially in the endemic regions. When the clinical suspicion exists detailed laboratory evaluation must be performed.

Phenotypic and Genotypic Correlation of Antimicrobial Susceptibility of Bacteroides fragilis: Lessons Learnt.

Background Bacteroides fragilis is an opportunistic pathogen causing severe infections, including bacteremia. There have been increased reports of antimicrobial resistance in B. fragilis. However, phenotypic testing of susceptibility is time consuming and not cost effective for anaerobes. The present study investigates the correlation of phenotypic susceptibility with genotypic markers; to determine if these could be considered for deciding empirical therapy for B. fragilis. Material and methods Bacteroides fragilis isolates from various clinical samples including exudates, tissue, and body fluids were collected between November 2018 and January 2020 in the Department of Clinical Microbiology, Christian Medical College (CMC) Vellore. Species identification was done by MatrixAssistedLaserDesorptionIonization time of flight mass spectrometry (MALDI TOF) according to the manufacturer's instructions. A total number of 51 B. fragilis isolates were tested against metronidazole, clindamycin, piperacillin/tazobactam, and meropenem phenotypically by agar dilution method using Clinical & Laboratory Standards Institute (CLSI) 2019 guidelines and minimum inhibitory concentrations (MIC) were interpretated. The genotypic markers for antimicrobial resistance genes (nim, emrF, and cfiA) were studied by polymerase chain reaction (PCR) assay as per the standard protocol on all isolates to detect resistance genes. Results B. fragilis isolates in this study expressed 45%, 41%, and 16% phenotypic resistance to clindamycin, metronidazole, and meropenem, respectively, with least resistance topiperacillin/tazobactam (6%). Among the metronidazole resistant isolates, 52% harbored nim gene. Nim gene was also present in 76% (23/30) of the metronidazole susceptible isolates. Similarly, cfiA was present in all eight meropenem resistant isolates in addition to 22% (9/41) of the susceptible isolates. All cfiA negative isolates were phenotypically susceptible. Interestingly, 74% (17/23) of the clindamycin resistant isolates were positive for ermF. Conclusions Detection of a limited set of genes does not always correlate with phenotypic resistance to metronidazole and clindamycindue to the reported influence of insertion sequence (IS) elements, efflux, and other genetic determinants. Certainly, the absence of the cfiA gene can be employed to rule out meropenem resistance. However, redundant use of antibiotics such as meropenem along with metronidazole could be avoided for B. fragilis, which might otherwise elevate meropenem resistance. Recommendation of metronidazole requires prior phenotypic testing due to the reported 41% resistance.

Antimicrobial Susceptibility Pattern in Opportunistic Pathogens Isolated from Immunocompromised Patients.

Brought with the advancements in transplantation science and the development of immunosuppressive agents, immunocompromised patients characterized with defective immunity have increased throughout the world with increased risk for opportunistic infections. This study provides an overview of the antimicrobial susceptibility pattern among opportunistic pathogens isolated from immunocompromised patients. Methods:Clinical and laboratory records of immunocompromised patients [patients with chronic kidney disease neutropenia, diabetes, rheumatic heart disease acquired immune deficiency syndrome hepatitis B, hepatitis C, who were subjected to microbiological culture analysis in the Department of Clinical Microbiology, KIST Medical College and Teaching Hospital, for 2 years (January 2019 and December 2020) were analyzed. Out of 8,402 immunocompromised patients, 954 (11.4%) patients were subjected to microbiological culture analysis. Among 954 patients, 253 (26.5%) patients [median(interquartile range) age: 52(31-67) years; male 138 (54.5%)] were infected. A total of 295 pathogens were isolated from 1,331 cultured samples. Infections due toEscherichia coli (n=71, 24.1%), Klebsiellaspp. (n=55, 18.6%),Acinetobacter calcoaceticus-baumannii complex (n=35, 11.9%), Candida albicans (n=30, 10.2%), and Staphylococcus aureus(n=28, 9.5%) were frequently observed. Among the bacterial isolates (n=239), 81.6% (n=195) of bacteria were β-lactamase producers, 51.0% (n=122) were multi-drug resistant, 9.2% (n=195) were extensively-drug resistant, 0.8% (n=195) were pan-drug resistant, and 35.7% (n=10) ofS. aureuswere methicillin-resistant Staphylococcus aureus. The majority of infection in immunocompromised patients is caused by Gram-negative bacteria, and is often associated with a higher number of β-lactamase producers and multi-drug resistant organisms. Prescriptions of antibiotics on the grounds of antimicrobial stewardship might help to reduce the burden of antimicrobial resistance.

Incidence, aetiology and temporal trend of bloodstream infections in southern Sweden from 2006 to 2019: a population-based study.

BackgroundBloodstream infections (BSI) are a public health concern, and infections caused by resistant bacteria further increase the overall BSI burden on healthcare.AimTo provide a population-based estimate of BSI incidence and relate this to the forthcoming demographic ageing western population change.MethodsWe retrieved positive blood cultures taken from patients in the Skåne region, southern Sweden, 2006-2019 from the Clinical Microbiology Department database and estimated incidence rates (IR), stratified by age (0-49, 50-64, 65-79, ≥ 80 years), sex, year, and species and described antimicrobial susceptibility for Enterobacterales.ResultsWe identified 944,375 blood culture sets, and 129,274 (13.7%) were positive. After deduplication and removal of contaminants, 54,498 separate BSI episodes remained. In total, 30,003 BSI episodes (55%) occurred in men. The overall IR of BSI was 307/100,000 person-years, with an average annual increase of 3.0%. Persons ≥ 80 years had the highest IR, 1781/100,000 person-years, as well as the largest increase. Escherichia coli (27%) and Staphylococcus aureus (13%) were the most frequent findings. The proportion of Enterobacterales isolates resistant to fluoroquinolones and third generation cephalosporins increased from 8.4% to 13.6%, and 4.9% to 7.3%, (p for trend < 0.001), with the largest increase in the oldest age group.ConclusionWe report among the highest BSI IRs to date worldwide, with a higher proportion among elderly persons and males, including resistant isolates. Given expected demographic changes, these results indicate a possible substantial future BSI burden, for which preventive measures are needed.