Concordance and discordance of GeneXpert MTB/RIF and conventional culture method for diagnosis of Extra-Pulmonary Tuberculosis at a tertiary care hospital in Pakistan.

Objective: To identify concordance and discordance between GeneXpert MTB/RIF assay and gold standard bacteriologic culture for the diagnosis of Mycobacterium tuberculosis (MTB) in Extra-Pulmonary tuberculosis (EPTB) specimens in our region. Methods: This is a retrospective cross-sectional study conducted at the Indus Hospital and Health Network. Data from 1st January, 2020 to 31st December, 2021 was analyzed. A total of 1499 EPTB specimens were included for which GeneXpert was requested along with acid-fast bacteria (AFB) culture from the same specimen. Specimens were processed according to specimen type following standard operating procedures of the laboratory. Fluorescent staining was performed on all specimens along with bacteriologic culture. The GeneXpert MTB/RIF assay was carried out in exact accordance with the manufacturer's instructions. Results: Out of 1499 EPTB specimens, 1370 (91.39%) specimens exhibited concordance between GeneXpert and conventional culture method, while 129 (8.60%) specimens showed discordance. GeneXpert exhibited sensitivity and specificity of 69.4% and 94.3% respectively in comparison to culture. Conclusion: GeneXpert sensitivity for the diagnosis of EPTB varied with the site involved. Lower sensitivity was observed in ascitic and pleural fluids as compared to higher sensitivity observed among urine samples and pus aspirates. However, given the quick turnaround time and ease of use, it is a helpful tool in the diagnosis of EPTB when utilized in the appropriate clinical context. Caution is advised while interpreting negative GeneXpert results in endemic settings and should be interpreted along with other supporting clinical and diagnostic features.

Cholera outbreak in 2022 among children in Karachi: Study of cases attending to a Tertiary Care Hospital.

Objective & Background: Repeated outbreaks of cholera have occurred in Karachi. Changing patterns in seasonality, serotypes and antibiotic resistance have been observed in these outbreaks. Recently, in the year 2022, a surge of cholera cases has been reported from Karachi during the months of April-June. This study aimed to identify clinical features, antibiotic susceptibility, complications, and response to treatment of V. cholerae infection among children attending Indus hospital, Karachi. Methods: A retrospective chart review of pediatric patients was conducted for children aged 0-16 years. All children treated for culture-proven cholera infection at Indus Hospital from March to June 2022 were included. Details of clinical features, complications, antibiotic susceptibility, and response to treatment were retrieved from the health management information system (HMIS) of the hospital. Results: Twenty children were included. The median age was 01 (0.50-3.75) years. There were 9 (45%) males and 11 (55%) females. All the culture isolates belonged to serogroup O1 Ogawa of the Vibrio cholerae. Vomiting and diarrhea were the most common symptoms. Dehydration, acute kidney injury, and shock were seen in 19 (95%), 6 (30%), and 2 (10%) children respectively. Eleven children were admitted with an average hospital stay of 5 (Median-IQR 3-6) days. The isolates were completely susceptible to tetracycline, ciprofloxacin, and azithromycin. Different antibiotics were given which included cefotaxime, ceftriaxone, doxycycline, and ciprofloxacin. All children responded completely to the antibiotics. Conclusion: In present study all V. cholerae isolates belonged to the O1 Ogawa serotype that showed complete susceptibility to tetracycline, ciprofloxacin, and azithromycin. Dehydration, electrolyte imbalance, and renal impairment were the most common complications observed. Drinking unboiled water was identified as a potential source of cholera in most children. Therefore, advocacy of hygienic practices and disinfection of water supplies is recommended to prevent future cholera outbreaks.

Determination of Inducible Clindamycin Resistance and Correlation with Vitek2 Inducible Clindamycin Resistance Test in Staphylococcus aureus Isolated from Clinical Samples.

OBJECTIVE: To compare the performance of Vitek2 with the gold standard D test in terms of inducible clindamycin resistance (ICR) detection. STUDY DESIGN: Descriptive study. Place and Duration of the Study: Indus Hospital and Health Network Karachi, Pakistan, from November 2021 to April 2022. METHODOLOGY: Standard operating procedures of the laboratory were followed for processing of clinical samples. Methicillin-resistant Staphylococcus aureus (MRSA) isolates were included. The isolates from the same patient within two-week time period were excluded. Clinical laboratory standards institute guidelines were followed for performing and interpreting D test. The results of the D test were compared with Vitek2 results for ICR. RESULTS: A total of 313 isolates were MRSA, of which 93 isolates tested positive for ICR on both the D test and Vitek2. Nine isolates were positive for ICR on Vitek2 and negative on the Kirby-Bauer disk diffusion method. One isolate tested positive on the disk method and negative on Vitek2. CONCLUSION: Vitek 2 appeared to give false positive results. Reporting false susceptibility of clindamycin can cause therapeutic failure which can markedly affect the patient's outcome. This discordance needs to be investigated further with a large sample size and stringent observation of D-test results to pick laboratory error. KEY WORDS: Methicillin-resistant Staphylococcus aureus, Inducible clindamycin resistance, D zone, Vitek2.

Cholera Outbreak 2022 in Karachi: A Report on Serotype and Antibiotic Susceptibility Pattern.

OBJECTIVE: To identify the bacterial agent responsible for the surge of cases of acute diarrhoeal disease in Karachi, Pakistan, and assess the antimicrobial susceptibility pattern of the isolates. STUDY DESIGN: Observational study. PLACE AND DURATION OF STUDY: Department of Microbiology, Indus Hospital & Health Network, Karachi, Pakistan, from 1st March to 31st May 2022. METHODOLOGY: Vibrio cholerae (V. Cholerae) isolates from stool samples received in the laboratory in the months of March, April, and May were identified and antibiotic susceptibility testing was performed by the Kirby-Bauer disk diffusion method. Serology was performed to identify the serotype causing a surge in cases of acute watery diarrhoea. RESULTS: A total of three-hundred and seventy-eight stool samples were received during the study period, out of which seventy-eight were positive for V. cholerae serogroup O1 serotype Ogawa. The isolate tested 100% sensitive for Ciprofloxacin, Tetracycline, Doxycycline, and Azithromycin, while 74% resistance was observed in Trimethoprim/Sulfamethoxazole and 25% resistance in Ampicillin. CONCLUSION: V. cholerae serogroup O1 serotype Ogawa was the causative agent responsible for cholera outbreak in Karachi during the early summer of 2022. Ciprofloxacin, Tetracycline, Doxycycline, and Azithromycin are appropriate antimicrobials for treatment; whereas resistance to Trimethoprim/Sulfamethoxazole, and Ampicillin was higher. KEY WORDS: Vibrio cholerae, Outbreak, Acute diarrhoeal disease.

Cystic Neutrophilic Granulomatous Mastitis.

Granulomatous lobular mastitis (GLM) is an infrequent inflammatory breast disease, which can simulate malignancy on the basis of clinical and imaging features. It is typically found in parous or lactating women. The differential diagnosis of granulomatous mastitis includes infections caused by bacterial, fungal or mycobacterial agents, and autoimmune disorders like rheumatoid arthritis, sarcoidosis, giant cell vasculitis, and granulomatosis with polyangiitis. Cystic neutrophilic granulomatous mastitis (CNGM) is a sporadic sub-type of GLM that can be linked with infection with Gram-positive bacilli, specifically, Corynebacterium. It is characterised by lipogranulomas that comprise of "cystic" spaces lined by neutrophils which may contain Gram-positive rod-shaped bacteria. The majority of cases of GLM are still "idiopathic" as this pattern of inflammation still remains a mystery. We herein report three cases of CNGM and review the relevant literature. Key Words: Granulomatous mastitis, Corynebacterium, Gram-positive rods, Inflammatory breast disease, Cystic neutrophilic granulomatous mastitis.