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Background The rise of Multidrug-resistant organisms (MDROs) poses a considerable burden on the healthcare systems, particularly in low-middle income countries like Pakistan. There is a scarcity of data on the carriage of MDRO particularly in the pediatrics population therefore, we aimed to determine MDRO carriage in pediatric patients at the time of admission to a tertiary care hospital in Karachi, Pakistan, and to identify the risk factors associated with it. Methods A cross-sectional study conducted at the pediatric department of Aga Khan University Hospital (AKUH) from May to September 2019 on 347 children aged 1–18 years. For identification of MDRO (i.e., Extended Spectrum Beta-Lactamase (ESBL) producers, Carbapenem Resistant Enterobacteriaceae (CRE), Vancomycin Resistant Enterococci (VRE), M ethicillin Resistant Staphylococcus aureus (MRSA), Multidrug-resistant (MDR) Acinetobacter species and MDR Pseudomonas aeruginosa ), nasal swabs and rectal swabs or stool samples were cultured on specific media within 72 h of hospitalization. Data was collected on a predesigned structured questionnaire on demographics, prior use of antibiotics for > 48 h in the last 6 months, history of vaccination in last 6 months, exposure to health care facility regardless of the time of exposure, ICU stay for > 72 h, and about the prior use of medical devices (urinary catheter, central venous lines etc.) in last 1 year. Statistical analysis was performed by Standard statistical software. Results Out of 347 participants, 237 (68.3%) were found to be MDRO carriers. Forty nine nasal swabs from 346 children (14.2%) showed growth of MRSA. The majority of the stool/rectal swabs ( n  = 222 of 322; 69%) collected were positive for MDRO. The most isolated species were ESBL Escherichia coli 174/222 (78.3%) followed by ESBL Enterobacter species 37/222 (16.7%) and ESBL Klebsiella pneumoniae 35/222 (15.8%). On univariate analysis, none of the risk factors showed statistically significant association with MDRO carriage. Conclusion Overall, a high prevalence of MDRO carriage was identified among admitted pediatric patients. Implementation of systematic screening may help to identify true burden of MDROs carriage in the health care settings.

Background and rationale Methicillin resistant Staphylococcus aureus (MRSA) colonization increases the risk of MRSA infection. Detecting MRSA colonization can influence postoperative outcomes and prolong hospital stay. The conventional standard culture method for detecting MRSA colonization has limitations in terms of sensitivity and turnaround time. Hence, we sought out use of Xpert PCR kit for prompt evaluation of MRSA colonization to support MRSA prevention in a tertiary care hospital in Karachi, Pakistan. Materials and methods During 1st April-31st December 2022, 290 nasal and skin swab samples were collected from 257 patients and processed using routine culture (as gold standard method) and PCR-based MRSA detection assay (MRSA Xpert). Results A total of two hundred and ninety (290) swab samples from 257 patients were obtained, 33 of which were paired. The overall prevalence of MRSA colonization was 12% by both methods, with 90% of cases classified as community-associated (CA-MRSA) whereas 10% as hospital-acquired (HA-MRSA). The colonized group showed a higher subsequent MRSA infection rate (11% vs. 3.5%) compared to the noncolonized group. Culture identified 11% of screening samples as MRSA positive, Xpert MRSA assay showed 100% sensitivity and 95% specificity. The cost of a single MRSA Xpert assay was $50 while MRSA culture cost around $7.50. Conclusion Our study findings suggest that the presence of MRSA colonization in our cohort of patients is consistent with the existing trends in hospital epidemiology. Both conventional culture and Xpert MRSA methods showed comparable efficacy for detection of MRSA colonization. Larger-scale studies are recommended to validate these findings conclusively.

We evaluated Salmonella enterica serotype Typhi strains isolated from all body sites in Pakistan during 2013-2018. Despite an increase in overall number of localized, extensively drug-resistant Salmonella Typhi in organ infections during 2018, there was no increase in the proportion of such isolates in comparison with non-extensively drug-resistant isolates.

Background Febrile neutropenia (FN) is a medical emergency in patients with acute leukemia (AL), which increases the risk of life-threatening infections. Emerging antimicrobial resistance (AMR) further complicates management. The study aims to identify pathogen frequency and antimicrobial susceptibility patterns. Methods A retrospective descriptive study was conducted at a tertiary care hospital from January 2020 to December 2023. Data on AL patients with FN were retrieved from the hospital information system using ICD codes. Results Of 478 FN episodes identified, 217 (45%) were microbiologically documented. The population consisted of 61.7% males, equally divided between adults (mean age, 38 years) and children (mean age, 8.4 years). AML was the predominant leukemia subtype (52.4%). Respiratory infections (40.5%) and gastrointestinal infections (33.6%) were the leading sources, with 21% having an unknown focus. Chest X-ray detected infection signs in 37.3% of episodes. Hospital stays exceeded 10 days in 67% of admissions, with mortality at 16.5%. A total of 335 pathogens were identified from 217 episodes, with 20.7% involving multiple infections and 4.6% polymicrobial. Gram-negative rods (GNRs) predominated (45.6%), followed by gram-positive cocci (GPCs) (30.7%), fungi (12.2%), viruses (7%), parasites (2.3%), and Mycobacterium tuberculosis (1.7%). Blood cultures yielded 71% of isolates. Leading GNRs were Escherichia coli (37.7%), Pseudomonas aeruginosa (14.5%), and Klebsiella species (13.2%). Among GPCs, Coagulase-negative staphylococci (CoNS) (41.1%), Enterococcus spp. (22.5%), and Staphylococcus aureus (18.6%) predominated. Common fungal pathogens included Aspergillus flavus complex (29.2%) and Candida parapsilosis (14.6%). Antimicrobial resistance among Enterobacterales was 77% to ceftriaxone, 63% to piperacillin–tazobactam, and 47% to carbapenems. Among GPCs, 95% of CoNS and 72% of S. aureus were methicillin-resistant; 76% of Enterococcus were vancomycin-resistant. Overall, 64% of isolates were MDR (62% GPCs, 65.6% GNRs). MDR infections had significantly higher mortality than non-MDR infections (14.0% vs. 3.5%, p  = 0.012). Meropenem and vancomycin were the most commonly used empiric agents in FN patients, each administered in 70% of the episodes, however 41% of the FN episodes were not adaequately covered by the empirical regimen. Conclusion FN in AL patients is frequently associated with infections with GNRs, with a high prevalence of MDR organisms contributing to increased mortality. Surveillance of pathogen distribution and resistance patterns is essential to guide empiric therapy and improve outcomes in this high-risk population. Clinical trial number Not applicable.

IntroductionVarious intracanal medicaments have been used in cases of chronic apical periodontitis for appropriate disinfection of the root canal system to eliminate microbes especially from the inaccessible areas. Calcium hydroxide is the most common intracanal medicament available in various forms, but its effectiveness with or without iodoform using microbial culture is unknown. Therefore, our aim is to compare the antimicrobial efficacy of Calcipex and Metapex in endodontic treatment of teeth presenting with chronic apical periodontitis by assessing the bacterial load reduction.Method and analysis60 single rooted teeth of patients with diagnosis of chronic apical periodontitis will be selected and the canals debrided chemomechanically. The patients will be randomised into two groups: Calcipex and Metapex. The first sample (S1) for bacterial culture will be taken before placement of intracanal medicament and the second sample (S2) will be taken after 7 days, before final obturation from the canal and sent to lab for culture. Colony-forming unit will be evaluated. Paired t-test will be used to assess difference between antimicrobial efficacies within the group of medicaments. Independent sample t-test will be used to assess antimicrobial efficacies between groups. Level of significance will be kept at 0.05.Ethics and disseminationApproval from Aga Khan University Hospital Ethical review committee is taken. Findings will be reported according to the Standard Protocol Items for Randomised Trials guidelines. Research findings will be disseminated through annual reports, peer-reviewed journals and conferences.Trial registration numberNCT04336709.

Background Enteric fever is an acute systemic infectious disease associated with substantial morbidity and mortality in low- and middle-income countries (LMIC), with a global burden of 14.3 million cases. Cases of enteric fever or paratyphoid fever, caused by Salmonella enterica serovar Paratyphi A ( S . Para A) have been found to rise in many endemic and non-endemic countries. Drug resistance is relatively uncommon in S . Para A. Here we report a case of paratyphoid fever caused by ceftriaxone resistant S . Para A from Pakistan. Case presentation A 29-year-old female presented with a history of fever, headache, and shivering. Her blood culture revealed a S . Para A isolate (S7), which was resistant to ceftriaxone, cefixime, ampicillin and ciprofloxacin. She was prescribed oral Azithromycin for 10 days, which resulted in resolution of her symptoms. Two other isolates of S . Para A (S1 and S4), resistant to fluoroquinolone were also selected for comparison. DST and whole genome sequencing was performed for all three isolates. Sequence analysis was performed for identification of drug resistance and phylogeny. Whole Genome Sequencing (WGS) of S7 revealed the presence of plasmids, IncX4 and IncFIB(K). blaCTX-M-15 and qnrS1 genes were found on IncFIB(K). The gyr A S83F mutation conferring fluoroquinolone resistance was also found present. Multi-locus sequence typing (MLST) showed the S7 isolate to belong to ST129. S1 and S4 had the gyr A S83Y and S83F mutations respectively. Conclusions We highlight the occurrence of plasmid-mediated ceftriaxone resistant strain of S . Para A. This is of significance as ceftriaxone is commonly used to treat paratyphoid fever and resistance in S . Para A is not known. Continuous epidemiological surveillance is required to monitor the transmission and spread of antimicrobial resistance (AMR) among Typhoidal Salmonellae. This will guide treatment options and preventive measures including the need for vaccination against S . Para A in the region.

Background Globally metronidazole and carbapenem resistance in anaerobic organisms is increasing necessitating continuous surveillance to guide selection of empirical treatment. In this study we have determined metronidazole resistance in anaerobes using MIC Evaluator strips (M.I.C.E strips). Carbapenem resistance was evaluated only in metronidazole resistant isolates. Material and methods The study was conducted at the Aga Khan University (AKU) Hospital laboratory, Karachi, Pakistan (2014–2017). Metronidazole and imipenem resistance was evaluated using M.I.C.E strips and minimum inhibitory concentrations (MICs) were interpreted using Clinical Laboratory Standards Institute (CLSI) criteria. Clinical details including demographics, prolonged hospital stay, malignancy, transplant, dialysis, diabetes, site of infection and outcome were analyzed for association with metronidazole resistance. Results Of the 223 clinically significant isolates, 39 (17.5%) were metronidazole resistant (excluding the inherently resistant organisms; for example Cutibacterium species). Imipenem resistance was determined in 29 metronidazole resistant isolates and of these 7 (24.1%) were found to be resistant. Proportion of metronidazole resistant strains was highest amongst Bacteroides species. A significant increase in metronidazole resistance from 12.3% in 2010–2011 to 17.5% in the current study was found. Carbapenem resistance also emerged in the period 2014–2017. Isolates from malignancy and transplant patients showed lower odds of developing metronidazole resistance (0.003(95% CI: 1.7–17.9)). Prolonged hospital stay was not associated with metronidazole resistance (1.1((95% CI: 0.5–2.5)). Conclusion The rising trend of metronidazole resistance and emergence of carbapenem resistance in anaerobic bacteria is alarming. Continued surveillance with strengthening of laboratory capacity regarding anaerobic susceptibility testing is urgently needed in Pakistan.

To describe an outbreak of Burkholderia cepacia complex at a tertiary care hospital in Karachi, Pakistan, highlighting contributing factors, potential sources, and system-level gaps identified during the investigation. Outbreak investigation. A 655-bed tertiary care teaching hospital in Karachi, Pakistan. All individuals who had positive blood cultures by non-lactose fermenting, oxidase-positive, Gram-negative rods that could not be further characterized. On September 26, 2020, the Department of Infection Prevention and Hospital Epidemiology (DIPHE) was notified of multiple positive blood cultures. An outbreak investigation was initiated, including chart reviews, laboratory analysis, environmental sampling, assessing central line insertion practices, and evaluating the manufacturing site. Clinical Laboratory Standards Institute (CLSI) guidelines were used for microbiological identification and susceptibility testing. Thirty-five patients with positive cultures were identified between September 15 and October 22, 2020. While environmental sampling did not yield growth, significant breaches at the suppliers' facility were identified in chlorhexidine gluconate (CHG) storage and quality control. Although cultures of CHG were negative, the product's withdrawal led to a marked decline in new cases. Moreover, while resources were unavailable for genomic testing, antimicrobial susceptibility patterns were similar in all the case strains, suggesting a common source. This outbreak highlights the role of contaminated disinfectants in healthcare-associated infections. It also revealed systemic gaps in disinfectant quality control, storage facilities, and diagnostic capacity, delaying outbreak recognition and response. It is essential to strengthen regulatory oversight, implement standardized testing protocols, and enhance microbiological diagnostic infrastructure to lower the risk of similar outbreaks.

Vancomycin-resistant enterococci (VRE) are one of the most common nosocomial infections. Linezolid has been used to treat such infections extensively. Over time there have been reports where linezolid resistance in enterococci has been documented. This is the first report from Pakistan where linezolid- and vancomycin-resistant Enterococcus faecium was isolated from cerebrospinal fluid (CSF) sample from infected ventriculoperitoneal (VP) shunt.