Cumulative antimicrobial susceptibilities for respiratory clinical isolates of Mycobacterium avium Complex, Mycobacterium kansasii, and Mycobacterium abscessus from Pakistan 2018 to 2022.

Background: Nontuberculous mycobacteria (NTM) are increasingly identified as causes of protracted pulmonary infections. Antibiotic susceptibility testing requires microdilution methods, which are often unavailable in laboratories in resource-poor settings. We report cumulative antibiograms for the most frequently isolated clinical pulmonary NTM from Pakistan to inform empiric antibiotic management of initial NTM infections. Methods: We analyzed data from 2018 to 2022 for the most frequently isolated and clinically relevant NTM isolated from respiratory specimens, i.e., Mycobacterium avium complex (MAC), Mycobacterium abscessus group (MAG), and Mycobacterium kansasii (MK). Antibiograms were developed using the Clinical Laboratory Standards Institute's M39ED5 standard. Percentage susceptibilities and 95% confidence intervals (CI) were calculated. Results: Over 4 years, 529 NTM, comprising 209 MAC, 249 MAG, and 71 MK were analyzed. For MAC and MAG, where clarithromycin (CLR)-based regimens are recommended, CLR was active for 94.8% (95% CI 91.3-96.9), and 77.5% (95% CI 71.4-82.7) isolates, respectively. Combination regimens comprising 3 active drugs CLR + linezolid (LZD) + moxifloxacin for MAC and CLR + LZD + Amikacin for MAG had 98.4% (95% CI 95.9-99.4) and 68.9% (95% CI 62.3-74.8) coverage for pulmonary disease, respectively. For MK, 91.5% (95% CI 82.8-96.1) isolates were susceptible to rifampin (RIF), with a combination of RIF + CLR covering 88.7% (95% CI 79.3-94.2) of MK pulmonary infections, respectively. Conclusions: These data can inform empiric treatment guidance for the most common NTM pulmonary infections, i.e., for MAC, MAG, and MK disease in Pakistan.

Etiology of Acute Infectious Meningitis and Meningoencephalitis in Karachi, Pakistan: Retrospective Observational Study from a Tertiary Care Center.

Meningoencephalitis (ME) is potentially fatal and is caused by a wide array of pathogens. Diagnostic and health-care access gaps prevent accurate estimation of the pathogen-specific burden in low-resource settings. We present pathogen-specific etiologies among patients hospitalized with ME in Karachi, Pakistan. We performed a retrospective hospital database evaluation of pathogen etiology and outcomes of community-acquired infectious ME at a single tertiary care center in Karachi, Pakistan. Annual rates of hospitalization (ARH) were calculated by adjusting for missed cases and are reported per 100,000 population. From May 2017 to April 2020, 522 episodes of infectious ME were identified in 514 patients. The overall ARH from ME was 5.7/100,000 population (95% CI, 5.1-6.1). Among children younger than 5 years, the ARH was 9.8/100,000 population (95% CI, 8.1-11.8). Unknown causes of ME resulted in the greatest burden, with an ARH of 1.9/100,000 population (95% CI, 1.7-2.2). Among known causes, the greatest burden of hospitalizations resulted from tuberculous ME (0.8/100,000; 95% CI, 0.6-0.97), followed by pneumococcal and enteroviral ME (both 0.6/100,000 population; 95% CI, 0.5-0.8). The burden of ME caused by pathogens preventable through vaccination or public health measures outweighed that of ME from other causes (P = 0.0092, Fisher's exact test). We report a broad range of pathogens causing ME in southern Pakistan and show a high burden of preventable illness. Synergistic actions to improve diagnostic strategies, increase vaccinations, and introduce measures to reduce water-borne and vector-borne diseases are required to reduce the ME burden in Pakistan and prevent future outbreaks.

Laboratory service relocation: experience and lessons learned from relocating a biosafety level-3 clinical mycobacteriology service to a new facility.

Objectives: We recount our experiences of relocating an active mycobacteriology reference level service in Karachi, Pakistan, from an older accredited biosafety level-3 facility to a newly constructed and environmentally validated facility. Methods: The service relocation planning, execution, and verification stages are described in detail. Results: Lessons learned from our experience include establishing a service transfer plan, including relevant service staff, obtaining their buy-in on the plan, arranging backup service facilities or liaisons for the execution phase, and ensuring viable backup arrangements for troubleshooting during the verification phase of services in the new facility. Careful planning and inclusion of all stakeholders are critical to avoid service interruptions. Conclusions: This narrative is expected to support other laboratorians, scientists, and clinicians providing laboratory services to large population sectors who are looking to move their services to a new location while continuing to offer said services in a proficient and reliable manner.

'Breakpoint broth microdilution plate' for susceptibility testing of Gram negative bacilli against colistin sulfate.

The MIC method applicable to Gram negative bacilli including Acinetobacter spp. is broth microdilution (BMD). Cost and/or availability issues limit the use of commercial MIC panels in resource limited settings. OBJECTIVES: To design and implement an in-house breakpoint BMD panel (BBMD) for colistin against Gram negative bacilli. DESIGN: BBMD panel was prepared in 96-well plate. MIC concentrations of 1, 2, & 4 â€‹µg/mL for test, and 0.25, 0.5, 1, 2 & 4 â€‹µg/mL for control strains were selected to accommodate 19 test and 3 quality control strains per plate. Plates were frozen at -80 â€‹°C until testing. Validation was performed using strains from a previously published study and compared with freshly prepared MIC panel of 16-0.03 â€‹µg/mL. RESULTS: Validation showed 100% agreement with the reference method and BBMD was introduced into routine laboratory practice for colistin susceptibility of carbapenem resistant Enterobacterales (CRE), Acinetobacter baumannii complex and Pseudomonas aeruginosa. From 2nd July-16th September 2018, a total of 1294 (mean 16.8 â€‹± â€‹5.5 isolates/day) clinical isolates were tested; 1157/1294 were reported (MIC ≤2 â€‹µg/mL) within 24-h, whereas 133 required resistance confirmation by full-range BMD. Resistance was confirmed for all but 24 isolates. These discrepancies were mostly due to contamination with bacterial genera inherently resistant to colistin. CONCLUSION: This BBMD plate is a high through-put and practical method that could reliably be utilized in a routine microbiology laboratory for colistin susceptibility testing of CRE, A. bauamanii complex and P. aeruginosa.