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.

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.

From mosquitoes to menace: Unveiling the dangers of West Nile virus in Pakistan.

Pakistan, a subtropical nation, has seen a rapid rise in Arboviral transmission in the past decade. Environmental hazards such as intense monsoon rains and yearly floods in addition to unsanitary living conditions pose an increased risk of arboviral infections. In recent years, the emergence and spread of West Nile virus (WNV), which can lead to a life-threatening meningoencephalitis, in Pakistan has alarmed the health care authorities of an impending outbreak. Health professionals and policymakers should give paramount importance to prevent its transmission across Pakistan as another arboviral outbreak would wreak havoc on the already fragile health infrastructure of the country. Proactive surveillance and prompt reporting are crucial for mitigating this threat as there are no vaccines available to prevent WNV infection.

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.

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.

Changing Trends Of Multidrug Resistant Bacteria: A Six Year Experience From A Tertiary Care Hospital.

BACKGROUND: There is a continuous increase in the number of bacteria showing resistance to various antibiotics, limiting the treatment options for infections. The objective of this study was to assess the trend in resistance pattern of multi drug resistant organisms over a period of 6 years. METHODS: A retrospective study was conducted in Indus Hospital and Health Network, Karachi, Pakistan from January 2014 to December 2019. Multidrug resistant organisms were isolated from various samples and the data of corresponding patients were extracted from electronic medical record. The patients of all age groups and either gender was included. Specimens were inoculated on Sheep Blood Agar, chocolate agar and MacConkey agar. Organisms were identified and antibiotic susceptibility testing was performed according to Clinical Laboratory Standard Institute guidelines. RESULTS: In 34628 cases, 5159 (14.8%) were isolated as MDR organisms. Out of these 44.2% were Gram negative, while 55.7% were Gram-positive bacteria. The highest MDR trend was observed for A. baumannii (0-70%) followed by MRSA (0-64%) P. aeruginosa (0-16%) Enterococcus (0-10%) CRE (2.8-5.8%). CONCLUSIONS: The continuous rising trend of multidrug resistant organisms has been observed during the period of our study. Therefore, there is an imperative need of constant monitoring and firm adherences to infection control strategies to avoid spread of MDR organisms.

Disseminated cryptococcal infection in a lymphoma suspected patient.

Cryptococcus neoformans is an opportunistic pathogen, mainly responsible for meningitis in immunodeficient individuals. We report a rare case of dessiminated cryptococcosis in a six years old boy, patient was being evaluated for lymphoma. In the present case the causative agent was Cryptococcus neoformans. It was diagnosed through Bactec, aerobic blood culture bottle. The cause of hospitalization of the patient was fever with abdominal pain. Blood and CSF culture revealed the presence of Cryptococcus neoformans which was further confirmed by urease test and corn meal tween agar (CMT). In the present case fungus was unusually isolated earlier from blood culture rather than cerebrospinal fluid.

Susceptibility pattern of Mycobacterium tuberculosis over a period of five years at Indus Hospital and Health Network, Karachi, Pakistan.

Objective: To determine the susceptibility pattern and frequency of isolation of multidrug, pre-extensively drug and extensively drug resistant TB in a tertiary care hospital in Karachi, Pakistan. Method: A cross-sectional study was designed. Samples received in the lab were processed for growth and sensitivity testing of Mycobacterium tuberculosis. Isolation of MTB was done on Mycobacteria growth indicator tube (MGIT) followed by identification using MPT64. Samples were than evaluated for drug sensitivity against first and second-line antimycobacterial drugs. Statistical analysis was performed using SPSS version 24.0. Results: Of the 20014 samples received, 23.1% were identified as Mycobacterium tuberculosis. Drug sensitivity testing was performed on 95.9% isolates. Fifty-two percent samples were from males and 48% female patients. The study found statistically non-significant relationship between gender and likelihood of disease with drug-resistant (DR)-MTB organisms. The rate of isolation of MDR-TB was highest (43%) among ages 25-55 years and previously treated patients compared to newly diagnosed patients (62% vs 36%). Among MTB positive samples, 91.5% were pulmonary while 8.5% were extrapulmonary samples. Extrapulmonary samples were more likely to be sensitive to antimycobacterial drugs. The highest resistance was observed against Isoniazid (pulmonary=58%; extrapulmonary=12.7%), Rifampicin (pulmonary=58.7%; extrapulmonary=8.2%), and Levofloxacin (pulmonary=29.2%; extrapulmonary=20%). Conclusion: A considerable number of drug resistant tuberculosis cases were identified in the present study. It is essential to develop further strategies to reduce the spread of this disease.