Identification of Peptoniphilus harei From Blood Cultures in an Infected Aortic Aneurysm Patient: Case Report and Review Published Literature

Gram-positive anaerobic cocci (GPAC) are a commensal part of human flora but are also opportunistic pathogens. This is possibly the first study to report a case of Peptoniphilus harei bacteremia in an abdominal aortic aneurysm (AAA) patient. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) failed to identify the isolate and molecular analysis confirmed it as P. harei. A comprehensive literature review revealed that P. harei is an emergent pathogen. This study serves as a reminder for practicing clinicians to include anaerobic blood cultures as part of their blood culture procedures; this is particularly important situations with a high level of suspicion of infection factors in some noninfectious diseases, as mentioned in this publication. Clinical microbiologists should be aware that the pathogenic potential of GPAC can be greatly underestimated leading to incorrect diagnosis on using only one method for pathogen identification. Upgradation and correction of the MALDI-TOF MS databases is recommended to provide reliable and rapid identification of GPAC at species level in medical diagnostic microbiology laboratories.

Melioidosis: A Neglected Infection in Bangladesh

Bangladesh is an example of a highly populous, agricultural country where melioidosis may be a significantly under diagnosed cause of infection and death. A recent regression model predicted 16,931 cases annually in Bangladesh with a mortality rate of 56%. However, we only manage to confirm (culture) around 80 cases in last 60 years. A lack of awareness among microbiologists and clinicians and a lack of diagnostic microbiology infrastructure are factors that are likely to lead to the underreporting of melioidosis. Melioidosis transmits through inoculation, inhalation and ingestion. Diabetes mellitus is the most common risk factor (12 times higher chance of getting the infection) predisposing individuals to melioidosis and is present in >50% of all patients. The clinical presentation is widely varied and can be mistaken for other diseases such as tuberculosis or more common forms of pneumonia giving rise to its nickname as the “great mimicker”. Disease manifestations vary from pneumonia or localized abscess to acute septicemias, or may present as a chronic infection. Culture is considered the current gold-standard for diagnosis and culture-confirmation should always be sought in patients where disease is suspected. It is strongly recommended that any non–Pseudomonas aeruginosa, oxidase-positive, Gram-negative bacillus isolated from any clinical specimen from a patient in an endemic area should be suspected to be Burkholderia pseudomallei (BP). In addition, based on antibiogram, any Gramnegative bacilli that are oxidase-positive, typically resistant to aminoglycosides (e.g., gentamicin), colistin, and polymyxin but sensitive to amoxicillin/clavulanic acid should be considered as BP. This bacteria is inherently resistant to penicillin, ampicillin, first generation and second-generation cephalosporins, gentamicin, tobramycin, streptomycin, and polymyxin. For intensive phase (10 to 14 days), ceftazidime or carbapenem is the drug of choice. For eradication phase (3 to 6 months), oral trimethoprim/ sulfamethoxazole is the drug of choice. Surgery (drainage of abscess) has an important role in the management of melioidosis. Preventive measures through protective gears could be useful particularly for the risk groups. J MEDICINE 2021; 22: 139-145

Fungal sinusitis post COVID 19 – A case series from a diagnostic microbiology laboratory

Fungal infections are on rise globally owing to use of immunosuppressant drugs for various diseases, increased use of antimicrobials and in-situ devices, long duration of stay in hospitalized patients. There was sharp rise in mucormycosis infections in patients post COVID 19 illness which were previously limited to patients of end stage diabetic ketoacidosis. We studied the epidemiological, clinical, microbiological and radiological aspects for culture positive cases of fungal sinusitis from April 2021 to June 2021. The mean age of our patients was 55.4 years (range 38 to 70 years). M:F ratio was 1.5:1. All fungal infections occurred in laboratory and/or radiologically diagnosed cases of COVID 1970% patients (n=7) had diabetes mellitus as co-morbidity. 60% of the cases (n=6) grew Rhizopus arrhizus, 30% grew Aspergillus species (n=3) and 10% grew Penicillium species (n=1). 90% of the cases (n=9) improved after treatment whereas 10% (n=1) succumbed to the illness.Along with rhino-orbito-cerebral mucormycosis infections, nasal aspergillosis was also noted as a prominent cause of fungal sinusitis in post COVID 19 illness. As the antifungal therapy for these two fungal infections differs significantly, caution must be adhered to while diagnosing and treating.

Metabolomics in the Diagnosis and Prognosis of COVID-19

Coronavirus disease 2019 (COVID-19) pandemic triggered an unprecedented global effort in developing rapid and inexpensive diagnostic and prognostic tools. Since the genome of SARS-CoV-2 was uncovered, detection of viral RNA by RT-qPCR has played the most significant role in preventing the spread of the virus through early detection and tracing of suspected COVID-19 cases and through screening of at-risk population. However, a large number of alternative test methods based on SARS-CoV-2 RNA or proteins or host factors associated with SARS-CoV-2 infection have been developed and evaluated. The application of metabolomics in infectious disease diagnostics is an evolving area of science that was boosted by the urgency of COVID-19 pandemic. Metabolomics approaches that rely on the analysis of volatile organic compounds exhaled by COVID-19 patients hold promise for applications in a large-scale screening of population in point-of-care (POC) setting. On the other hand, successful application of mass-spectrometry to detect specific spectral signatures associated with COVID-19 in nasopharyngeal swab specimens may significantly save the cost and turnaround time of COVID-19 testing in the diagnostic microbiology and virology laboratories. Active research is also ongoing on the discovery of potential metabolomics-based prognostic markers for the disease that can be applied to serum or plasma specimens. Several metabolic pathways related to amino acid, lipid and energy metabolism were found to be affected by severe disease with COVID-19. In particular, tryptophan metabolism via the kynurenine pathway were persistently dysregulated in several independent studies, suggesting the roles of several metabolites of this pathway such as tryptophan, kynurenine and 3-hydroxykynurenine as potential prognostic markers of the disease. However, standardization of the test methods and large-scale clinical validation are necessary before these tests can be applied in a clinical setting. With rapidly expanding data on the metabolic profiles of COVID-19 patients with varying degrees of severity, it is likely that metabolomics will play an important role in near future in predicting the outcome of the disease with a greater degree of certainty.

Molecular genetic techniques in current biomedical research. Part II: PCR applications in diagnostics of human infectious diseases

Polymerase chain reaction (PCR)-based diagnostics is currently established as a gold standard for the detection of microorganisms. The features of PCR include rapid amplification of DNA and RNA as well as high sensitivity and specificity. In contrast to diagnostic microbiology, PCR diagnostics does not require preliminary culture of the microorganisms for their identification, reducing both time and costs of the diagnostic procedure. The lecture discusses the molecular basis behind the modern technical solutions for the PCR diagnostics of human infectious diseases including multiplex and reverse transcription PCR. We describe the principles of qualitative and quantitative PCR-based detection of pathogens in biological samples and provide the examples of PCR application for solving specific diagnostic scenarios. The lecture is primarily designed for students of biomedical specialties and healthcare professionals using molecular genetic techniques in their practice.

Concomitant Burkholderiapseudomallei and Staphylococcus aureus Infection in a chronic kidney disease patient: A Case Report and Literature Review

Melioidosis can happen in humans and animals. It has a wide range of clinical presentations that include asymptomatic infection, ulcers or abscesses of the skin, pneumonia, and multiple internal organ abscesses that may lead to fulminant septic shock. The organism presence in soil and surface of the water. We present a case of a non-diabetic chronic kidney disease patient presented with multiple carbuncles and respiratory melioidosis in which we are able to isolate B. pseudomallei after prolonging the plate incubation for 48-hours. We also suggested available tests in most diagnostic microbiology laboratory for identification of the organism. Bangladesh Journal of Medical Science Vol.20(2) 2021 p.456-458

High burden of infections caused by ESBL-producing MDR Escherichia coli in paediatric patients, Yangon, Myanmar

Background There is mounting evidence of a high burden of antimicrobial-resistant infections in children in low- and middle-income countries (LMICs). Objectives To detect the frequency of ESBL-producing Escherichia coli in clinical specimens from paediatric patients attending Yangon Children’s Hospital in Myanmar. Methods All children attending Yangon Children’s Hospital who had clinical specimens submitted to the hospital diagnostic microbiology laboratory from June 2019 to December 2019 were included in the study. Specimens were processed routinely using standard methods with BD Phoenix used for pathogen identification and susceptibility testing. Presence of ESBLs was determined using the cephalosporin/clavulanate combination disc method with confirmation by PCR. Results From 3462 specimens submitted to the Microbiology Laboratory, a total of 123 E. coli were isolated. Among them, 100 isolates were phenotypically ESBL producers, 94 (76.4%) of which were confirmed by PCR [82/94 (87%) CTX-M, 72/94 (77%) TEM, 1/94 (1%) SHV]. Most of the ESBL-producing E. coli were isolated from urine samples (52.1%, 49/94) and the majority were from the surgical unit (61.7%, 58/94). Only 34/94 (36%) isolates were susceptible to meropenem. Conclusions This study confirms a high proportion of infections caused by ESBL-producing and MDR E. coli in children hospitalized in Yangon, where access to effective second-line antimicrobials is limited.