Fungal empyema thoracis, a rare but an emerging entity: a retrospective case series from Pakistan.

Background and objective: Fungal empyema is a rare entity which is associated with high mortality. It is mostly seen in immune-compromised hosts. However, there is limited data available on fungal empyema from developing countries regarding risk factors, treatment, and outcome. This study was conducted to determine the risk factors, clinical features, treatment, and outcome of fungal empyema. Methods: A retrospective observational study was performed on proven fungal empyema cases, admitted at Aga Khan University Hospital, Karachi, Pakistan during January 2018 to May 2021. We excluded all those patients with polymicrobial bacterial and fungal empyema or with negative pleural fluid cultures. A preformed questionnaire was filled out for each case. Results: A total of 26 patients were diagnosed with fungal empyema with a mean age of 43.6 ± 20.3 years. Of these, 16 (61.5%) patients were male. Diabetes mellitus was the most frequent comorbidity (n = 11, 42.3%), followed by hypertension (n = 9, 34.6%), malignancy (n = 6, 23.1%), and asthma (n = 1, 3.8%). Ten (38.5%) patients had multiple comorbidities. Candida spp. was isolated in 21 (80.8%) patients and Aspergillus spp. in 7 (26.9%) patients. Fusarium spp. was isolated from one (3.9%) patient. Video-assisted thoracoscopy surgery was done in 14 (53.8%) patients and 12 (46.1%) patients were managed with tube thoracostomy. Twenty-one (80.8%) patients received antifungal agents. Overall, in-hospital mortality was 38.5% (n = 10) and all patients developed respiratory failure. Clinical improvement was seen in 16 (61.5%) patients. Conclusion: Our data suggest that fungal empyema has a poor outcome as almost one-third of our patients died. Early diagnosis and intervention can improve outcome.

Fungal Empyema; A Case series from Pakistan • This study was carried out as there are limited data available globally on fungal empyema. • We conducted a retrospective case study of 26 patients and our findings suggest that the fungal empyema has a poor outcome. • One third of our patients died during hospital stay. • Early diagnosis and treatment are important in fungal empyema. • Diabetes mellitus was found as a possible risk factor for fungal empyema, which should be evaluated further in future studies.

Allergic bronchopulmonary aspergillosis: radiological and microbiological profile of patients presented in an outpatient pulmonary clinic in a developing country.

There is limited data available about allergic bronchopulmonary aspergillosis (ABPA) in Pakistan. The aim of the study was to describe the radiological and microbiological profile of ABPA patients presenting to the outpatient pulmonary clinic of a tertiary care hospital in Karachi, Pakistan. A retrospective study was conducted on ABPA patients who presented to the pulmonary outpatient clinic at Aga Khan University Hospital, Karachi, Pakistan, from January 2017 to December 2019. Data was collected on microbiology and radiology features on predesigned proforma. A total of 7759 asthmatic patients presented at the outpatient pulmonology clinic during the study period. Of the 245 patients labeled as ABPA, 167 fulfilled the inclusion criteria, and 91 (54.5%) were female (mean age 41.9±13.0 years). A high resolution computed tomography scan of the chest was available for 126 patients. Of these, 104 (82.5%) patients had bronchiectasis. Central bronchiectasis was noted in 98 (94.2%), mucus plugging in 71 (56.3%), and hyperinflation was seen in 30 (23.4%) patients. Microbiological testing was available in 103/167 (61.7%) patients. The most common bacterial pathogen was Pseudomonas aeruginosa 32 (31.1%), followed by Hemophilus influenzae 16 (15.5%), and Moraxella catarrhalis 7 (9.7%). Aspergillus fumigatus 17 (23.6%) was the most common mold, followed by Aspergillus flavus 16 (22.2%) and Aspergillus niger 11 (15.3%). Co-infection (bacterial and fungal) was found in 18 (17.45%) patients. Bronchiectasis was frequently observed in our cohort of patients with ABPA. Pseudomonas aeruginosa was found to be common among bacterial pathogens. Isolation of fungus is not uncommon in these patients.

The current state of laboratory mycology in Asia/Pacific: A survey from the European Confederation of Medical Mycology (ECMM) and International Society for Human and Animal Mycology (ISHAM).

INTRODUCTION: Invasive fungal infections (IFIs) in Asia/Pacific are a particular threat to patients with malignancies, uncontrolled diabetes mellitus or undiagnosed/untreated human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS). Adequate and early access to diagnostic tools and antifungals is essential for IFI clinical management and patient survival. METHODS: Details on institution profile, self-perception on IFI, and access to microscopy, culture, serology, antigen detection, molecular testing, and therapeutic drug monitoring for IFI were collected in a survey. RESULTS: As of June 2022, 235 centres from 40 countries/territories in Asia/Pacific answered the questionnaire. More than half the centres were from six countries: India (25%), China (17%), Thailand (5%), Indonesia, Iran, and Japan (4% each). Candida spp. (93%) and Aspergillus spp. (75%) were considered the most relevant pathogens. Most institutions had access to microscopy (98%) or culture-based approaches (97%). Furthermore, 79% of centres had access to antigen detection, 66% to molecular assays, and 63% to antibody tests. Access to antifungals varied between countries/territories. At least one triazole was available in 93% of the reporting sites (voriconazole [89%] was the most common mould-active azole), whereas 80% had at least one amphotericin B formulation, and 72% had at least one echinocandin. CONCLUSION: According to the replies provided, the resources available for IFI diagnosis and management vary among Asia/Pacific countries/territories. Economical or geographical factors may play a key role in the incidence and clinical handling of this disease burden. Regional cooperation may be a good strategy to overcome shortcomings.

Open Online Courses for Strengthening Laboratory-Based Detection of Antimicrobial Resistance in Pakistan.

Introduction: Quality-assured antimicrobial susceptibility testing (AST) depends upon the knowledge and skills of laboratory staff. In many low- and middle-income countries (LMICs), including Pakistan, such types of knowledge and skills are limited. Therefore, the objective of this study was to use openaccess online courses to improve the knowledge of laboratory staff involved in the detection and reporting of antimicrobial resistance (AMR). Methodology: Seven online modules comprising 22 courses aimed at strengthening the laboratory detection of Antimicrobial resistance (AMR) were developed. The courses were uploaded onto the website www.parn.org.pk. Participants had an option of selecting courses of their interest. Online registration and completion of a pre-course assessment (pre-test) were essential for enrolment. However, participation in post-course assessment (post-test) was optional. The number of registered participants and the proportion of participants who completed each course were computed. A paired t-test was used to assess the increase between mean pre- and post-test scores. The association between the participants working in public vs. private laboratories and course completion rates were determined using the chi-square test. Results: A total of 227 participants from Pakistan (March 2018 to June 2020) were registered. The largest number of registered participants and the highest completion rate were noted for AST and biosafety courses, while quality-related courses attracted a lower interest. A comparison of pre- and post-test performance using the paired mean score for the individual courses showed a statistically significant (the value of p < 0.05) improvement in 13/20 assessed courses. A higher course completion rate was observed in participants from public vs. private sector laboratories (56.8 vs. 30.8%, the value of p = 0.005). Conclusions: Our study suggests a promising potential for open online courses (OOCs) toward addressing knowledge gaps in laboratory practice in resource limited settings.

A Review of Coronaviruses Associated With Kawasaki Disease: Possible Implications for Pathogenesis of the Multisystem Inflammatory Syndrome Associated With COVID-19.

Multisystem Inflammatory Syndrome in Children (MIS-C), representing a new entity in the spectrum of manifestations of COVID-19, bears symptomatic resemblance with Kawasaki Disease (KD). This review explores the possible associations between KD and the human coronaviruses and discusses the pathophysiological similarities between KD and MIS-C and proposes implications for the pathogenesis of MIS-C in COVID-19. Since 2005, when a case-control study demonstrated the association of a strain of human coronavirus with KD, several studies have provided evidence regarding the association of different strains of the human coronaviruses with KD. Thus, the emergence of the KD-like disease MIS-C in COVID-19 may not be an unprecedented phenomenon. KD and MIS-C share a range of similarities in pathophysiology and possibly even genetics. Both share features of a cytokine storm, leading to a systemic inflammatory response and oxidative stress that may cause vasculitis and precipitate multi-organ failure. Moreover, antibody-dependent enhancement, a phenomenon demonstrated in previous coronaviruses, and the possible superantigenic behavior of SARS-CoV-2, possibly may also contribute toward the pathogenesis of MIS-C. Lastly, there is some evidence of complement-mediated microvascular injury in COVID-19, as well as of endotheliitis. Genetics may also represent a possible link between MIS-C and KD, with variations in FcγRII and IL-6 genes potentially increasing susceptibility to both conditions. Early detection and treatment are essential for the management of MIS-C in COVID-19. By highlighting the potential pathophysiological mechanisms that contribute to MIS-C, our review holds important implications for diagnostics, management, and further research of this rare manifestation of COVID-19.

Heating effect on quality characteristics of mixed canola cooking oils.

BACKGROUND: The subcontinent is famous for its variety of seasonal foods cooked in vegetable seed cooking oils at elevated heating. Oils are often of poor quality that effect to consumer health. The work, therefore, planned to examine the effects of heat on the quality of mixed canola cooking oils (MCCOs). MCCOs were analyzed by preparing volatile fatty acid methyl esters (FAMEs) and for physiochemical properties. RESULTS: A major change was observed in the FAs composition of various MCCOs as coded K-1 to K-5. MCCOs were found rich in unsaturated 9-octadecanoic acid (oleic acid C18:1) and 9, 12-octadecadienoic acid (linoleic acid C18:2) along saturated octadecanoic acid (stearic acid C18:0). Results reveals that canola oil samples are mixed in the range of 4-30% with other vegetable oils and animal fats. The quality of canola cooking oils further reduced after heating to 100 °C, 200 °C and 350 °C, respectively. Quality parameters of MCCOs were significantly altered after heating and found as color (510-520 nm to 570-600 nm), mass 220-237 g to 210-225 g, volume 250 mL to 239 mL, pH (6.76-6.89), specific gravity (0.87-0.92), refractive index (1.471-1.475), saponification value (SV) (0.7-2.5), un-saponifiable matter (2.4-9.8%) and acid value (AV) (1.20-5.0 mg KOH). CONCLUSION: Heating of oils at elevated temperature have shown a significant effect on pH, specific gravity and un-saponifiable matter (p-value < 0.05). Large changes in the physicochemical parameters and FAs composition help to develop a conclusion that cooking at high temperatures affects the quality of mixed canola cooking oils.

Invasive pulmonary aspergillosis in critically ill patients with pneumonia due to COVID-19, influenza, and community-acquired pneumonia: A prospective observational study.

Background and Purpose: Influenza A and SARS-CoV-2 are risk factors for invasive pulmonary aspergillosis. Both influenza-associated pulmonary aspergillosis and COVID-19-associated pulmonary aspergillosis result in high mortality and poor clinical outcomes. No prospective study has so far compared the features, treatment, and outcomes of influenza-associated pulmonary aspergillosis and COVID-19-associated pulmonary aspergillosis within a similar time frame. Therefore, this study aimed to determine the frequency, risk factors, and outcomes of invasive pulmonary aspergillosis in critically ill patients with influenza, COVID-19, and community-acquired pneumonia. Materials and Methods: This prospective study included adult patients with pneumonia and was conducted at The Aga Khan University Hospital in Karachi, Pakistan. Patients were divided into three groups, including community-acquired pneumonia, influenza pneumonia, and COVID-19 pneumonia. The data collected included information on demographic characteristics, comorbidities, clinical features, laboratory results, treatment, and outcomes. Results: A total of 140 patients were included in this study. These included 35 (25%), 70 (50%), and 35 (25%) patients with community-acquired pneumonia, influenza pneumonia, and COVID-19 pneumonia, respectively. In addition, 20 (14.2%) patients were found to have invasive aspergillosis, of whom 10/35 (28.5%), 9/70 (12.8%), and 1/35 (2.8%) patients were in the COVID-19, influenza, and community-acquired pneumonia groups, respectively. Moreover, nine (90%) COVID-19-associated pulmonary aspergillosis patients required vasopressors, compared to three (33%) patients with influenza-associated pulmonary aspergillosis (P=0.020). In total, seven (70%) COVID-19-associated pulmonary aspergillosis patients required invasive mechanical ventilation compared to four (44%) influenza-associated pulmonary aspergillosis patients (P=0.37). The mean±SD length of hospital stay was highest in the COVID-19-associated pulmonary aspergillosis patients (18.3±7.28 days) compared to influenza-associated pulmonary aspergillosis patients (11.7±5.34 days) (P=0.036). The number of deaths in influenza-associated pulmonary aspergillosis and COVID-19-associated pulmonary aspergillosis patients was three (33.3%) and five (50%), respectively (P=0.526). Conclusion: A higher proportion of patients with COVID-19 developed invasive aspergillosis compared to those with influenza. Although the mortality rate in COVID-19-associated pulmonary aspergillosis was comparable to that in influenza-associated pulmonary aspergillosis patients, COVID-19-associated pulmonary aspergillosis patients had a significantly longer stay in the hospital.

Online assessment in undergraduate medical education: Challenges and solutions from a LMIC university.

BACKGROUND AND OBJECTIVES: The Covid-19 pandemic has caused large-scale disruption in almost all educational programs across the world. Planning and rapid implementation of assessment through an online format presents the next set of novel challenges that must be addressed by academic administrations across the globe. METHODS: This cross-sectional study was conducted between March to August 2020 at the Aga Khan University Medical College. Two hundred medical students of year 1 and 2 participated in the study. We describe the planning, processes, and outcomes of online assessments using video communication platforms conducted at a private university in Pakistan. Standardized protocols were written and piloted, extensive training of student, proctors and staff for preparation and conduct of online assessments were developed. Feedback was recorded after each session and suggestions were incorporated in subsequent high-stakes assessments. RESULTS: A total of three pilot assessments were conducted to identify issues and process refinement. Commercially available lockdown browser and ZOOM were used in the first pilot; 80% of the class was unable to launch lockdown browser and laptops required repeated reload/reboot. For the second pilot assessment, University's VLE page & MS Teams was trailed. Issues with internet connectivity, VLE page slowdown, and suboptimal recording feature in MS Teams were identified. For the final pilot assessment, phased launching of VLE page with single test item per page was implemented with success. The students reported that attempting the online exam on VLE with ZOOM support was user friendly. Ninety percent of the class was supportive of the continuing with the online assessments. CONCLUSION: In order to device an effective protocol for e-assessments conducting multiple trial runs, and incorporating feedback from all stakeholders is a necessity.

Respiratory pathogens in patients with acute exacerbation of non-cystic fibrosis bronchiectasis from a developing country.

Bronchiectasis unrelated to cystic fibrosis (non-CF bronchiectasis) has become a major respiratory disease in developing nations. The dilated mucus filled airways promote bacterial overgrowth followed by chronic infection, bronchial inflammation, lung injury and re-infection. Accurate pathogen identification and antimicrobial susceptibility allowing appropriate treatment, in turn, may break this vicious cycle.  This study aimed to gain kowledge about the spectrum and antimicrobial spectrum of pathogen yielded from respiratory specimens in adult patients with acute exacerbation of non-cystic fibrosis (CF) bronchiectasis. This cross-sectional study was performed at the pulmonology clinics of the Aga Khan University, Karachi, Pakistan from 2016-2019. Respiratory specimens were collected from adult patients with acute exacerbation of non-CF bronchiectasis presenting in pulmonology clinics. Microbial cultures were performed using standard methodology. Susceptibility testing was performed and interpreted using Clinical Laboratory Standard Institute criteria.  A total of 345 positive cultures from 160 patients presenting with acute exacerbation were evaluated. The most frequent organisms were Pseudomonas aeruginosa (n=209) followed by Hemophilus influenzae (n=40) and Staphylococcus aureus (n=24). High rates of antimicrobial resistance were found in all these pathogens. Proportion of Pseudomonas aeruginosa strains resistant to ciprofloxacin, imipenem, ceftazidime and piperacillin-tazobactam were 27.1%, 16.8%, 14.8% and 13.1% respectively. 65% of Hemophilus influenzae strains were resistant to cotrimoxazole and ciprofloxacin and 66.7% of Staphylococcus aureus strains were resistant to methicillin. High antimicrobial resistance in non-CF bronchiectasis patients against commonly used antimicrobials is a concern and highlight need for urgent community level interventions to improve clinical outcome in these patients.

Efforts to improve diagnosis of bacteraemia by reducing blood culture contamination in an emergency department: strategies and outcome.

OBJECTIVE: To assess the strategies and outcome for reducing blood culture contamination in order to improve the diagnosis of bacteraemia. METHODS: The interventional study was conducted at a tertiary care hospital in Karachi from January 1, 2013, to December 31, 2016. The blood culture contamination data related to the first year of the study was taken as the baseline pre-intervention data. Strategies were planned as intervention for improvement by consolidating training and education in the form of dedicated lectures, practising on mannequins and developing in-house video, replacing povidone with 2% chlorhexidine preparation spray plus 70% isopropyl alcohol swabs and inducting dedicated phlebotomy team whose only responsibility was blood sample collection and minimising the probability of error. RESULTS: In 2013, there were 8868 samples; 7402 in 2014; 6897 in 2015; and 9756 samples in 2016. The contamination rate in 2013 was 8% which went down to 7.75% in 2014, 4.25% in 2015 and 3.9% in 2016. The decline became statistically significant (p<0.001) after implementing a dedicated phlebotomy team in the emergency department. CONCLUSIONS: Apart from teaching and training, the concept of blood culture collection kit with checklist and dedicated blood collection team was found to be vital in reducing blood culture contamination.

Clinical spectrum and factors impacting outcome of Candida auris: a single center study from Pakistan.

BACKGROUND: An outbreak of Candida auris began globally in 2014 including Pakistan and since then it has emerged as a nosocomial multi-drug resistant pathogen. The aim of this study was to assess the clinical spectrum and outcome of patients, from a single center in Pakistan, in whom C. auris was isolated. METHODS: A retrospective study was conducted on 92 patients; ≥16 years with at least one culture positive for C. auris, at the Aga Khan University Hospital Karachi, Pakistan from Sept 2014-Mar 2017.Demographics, clinical history, management and outcome were studied. A logistic regression model was used to identify the risk factors for mortality. RESULTS: We identified 92 patients with C. auris (193 isolates), of whom 52.2% were males. Mean age was 54.14 ± 20.4 years. Positive cultures were obtained after a median hospital stay of 14 days. Most patients had a history of surgery (57.6%), antibiotic use (95.6%), ICU stay (44.6%), indwelling lines (88.04%) and isolation of another multi-resistant organism (52.2%).Most patients were symptomatic (70.7%). Amongst these, 38 had candidemia while 27 had non-candidemia infections. Sites of infection included central lines (35), urinary tract (19), peritonitis (4), nosocomial ventriculitis (1), empyema (1), fungal keratitis (1) otitis externa (1) and surgical site (1). Fluconazole resistance was 100% while 28.5 and 7.9% were Voriconazole and Amphotericin resistant respectively. Overall crude mortality was 42.4% while 14-day mortality was 31.5%. Both infected and colonized cases shared similar mortality (46.2% vs 33.3%; p-value = 0.25). Among infected cases mortality was high in candidemia compared to non-candidemia (60.5% vs 25.9%) in which deaths related to C. auris were 34.2% vs 22.2% respectively. On multivariate analysis candidemia (AOR 4.2, 95% CI: 1.09-16.49; p-value = 0.037) was associated with greater mortality with source control being the only protective factor for mortality (AOR 0.22, 95% CI: 0.05-0.92; p-value0.038] while ICU stay, rapidity of blood culture clearance, DM, malignancy and MDR co-infection had no impact. CONCLUSION: Patients with C.auris from a single center in Pakistan have a wide clinical spectrum with line associated infection being the predominant site of infection. Candidemia leads to high mortality while source control improves outcome.

Factors associated with onychomycosis in nail psoriasis: a multicenter study in Pakistan.

BACKGROUND: Treatment of psoriatic nail disease is challenging, and dystrophic psoriatic nails can get secondarily infected with fungi. METHODS: This 2-year, matched case-control study was conducted at three tertiary care centers of Karachi, Pakistan. Data were collected from patients with nail psoriasis as cases with age- and gender-matched controls. A detailed questionnaire was filled for all study participants. Nail Psoriasis Severity Index (NAPSI) scoring tool was used to assess dystrophy. Fungal infection was inferred by nail clippings for fungal hyphae and culture. RESULTS: Among 477 participants, 159 cases and 318 controls completed the study. Their mean age was 44 years, and one-third were female. Fungal culture positivity was statistically significant in cases as compared to the control group (P < 0.001). The most frequent species identified was Candida parapsilosis in both cases and controls. Body mass index, NAPSI scoring, socioeconomic status, elevated diastolic blood pressure, smoking status psoriasis among first-degree relatives, and longstanding disease of more than 10 years were significant factors in univariable analysis. Multivariable logistic regression identified independent factors like low to middle socioeconomic status, history of psoriasis in first-degree relative, current smoker, and obesity. CONCLUSION: We found nearly one-third of the psoriatic patients with nail involvement having concomitant fungal infection. We emphasize that nail clipping for fungal smear and culture should be advised to those patients with coexisting factors found significant in our study results. This opinion can be incorporated in psoriasis management guidelines for improving treatment of psoriatic nails.

Non-surgical management of caesarean scar ectopic pregnancy - a five-year experience.

The aim of this paper is to review the diagnosis and treatment of patients with a caesarean scar pregnancy (CSP), who have been managed at our unit, as well as to evaluate the effectiveness of the non-surgical treatment options. Twenty-six cases were identified over a period of 5 years and 4 months (January 2012 until April 2017). The main outcome measures were a number of previous caesarean births, a method of diagnosis of CSP, the mode of treatment and the outcome. The diagnostic criteria on the ultrasound were an empty uterine cavity and cervical canal, the presence of a gestational sac anterior to the isthmic portion of the uterus, an absent or thinned (<5 mm) myometrial thickness between the gestational sac and the bladder, with a peri-trophoblastic circulation around the gestational sac with the colour flow Doppler examination. The diagnosis was confirmed using ultrasound in 25 of the cases (96%) and by laparoscopy in one patient (4%). Fourteen women (54%) were managed conservatively, as there was evidence of a spontaneous resolution. A systemic methotrexate injection was used successfully to treat 11 (42%) patients. Only one patient (4%) needed an additional surgical treatment following an incomplete resolution. Impact Statement What is already known on this subject? A caesarean scar pregnancy is a life threatening condition whose incidence is increasing due to the global increase in the number of caesarean deliveries. Due to the relative rarity of the condition there is no consensus regarding the management of these cases. The management is mainly individualised, depending upon both the gestation and clinical symptoms. Surgical management or an intra-gestational sac injection of methotrexate with or without potassium chloride (KCl) dominates most of the published case reports and the systemic reviews. What the results of this study add? All of our patients in this case series were managed either conservatively with active monitoring, or were treated with an intramuscular methotrexate injection. Only one patient needed an additional minor surgical procedure due to an incomplete medical management. These results are very encouraging, and are attributed to the early diagnosis followed by a prompt treatment. An early detection requires a high index of suspicion, strict diagnostic criteria, and properly trained, experienced sonographers. A complete resolution was slow in some cases but the major high risk surgical procedures were avoided. What the implications are of these findings for clinical practice and/or further research? We wanted the sharing of our experience via this review to play a positive role in guiding the treatment of this rare but increasing subset of ectopic pregnancies.

Readiness for antimicrobial resistance (AMR) surveillance in Pakistan; a model for laboratory strengthening.

BACKGROUND: Limited capacity of laboratories for antimicrobial susceptibility testing (AST) presents a critical diagnostic bottleneck in resource limited countries. This paper aims to identify such gaps and to explore whether laboratory networks could contribute towards improving AST in low resource settings. METHODS: A self-assessment tool to assess antimicrobial susceptibility testing capacity was administered as a pre-workshop activity to participants from 30 microbiology laboratories in 3 cities in Pakistan. Data from public and private laboratories was analyzed and capacity of each scored in percentage terms. Laboratories from Karachi were invited to join a support network. A cohort of five laboratories that consented were provided additional training and updates sessions over a period of 15 months. Impact of training activities in these laboratories was evaluated using a point scoring (0-11) tool. RESULTS: Results of self-assessment component identified a number of areas that required strengthening (scores of ≤60%). These included; readiness for AMR surveillance; 38 and 46%, quality assurance; 49 and 55%, and detection of specific organisms; 56 and 60% for public and private laboratories respectively. No significant difference was detected in AST capacity between public and private laboratories [ANOVA; p > 0.05]. Scoring tool used to assess impact of training within the longitudinal cohort showed an increase from a baseline of 1-5.5 (August 2015) to improved post training scores of 7-11 (October 2016) for the 5 laboratories included. Moreover, statistical analysis using paired t-Test Analysis, assuming unequal variance, indicated that the increase in scored noted represents a statistically significant improvement in the components evaluated [p < 0.05]. CONCLUSION: Strengthening of laboratory capacity for AMR surveillance is important. Our data shows that close mentoring and support can help enhance capacity for antimicrobial sensitivity testing in resource limited settings. Our study further presents a model wherein laboratory networks can be successfully established and used towards improving diagnostic capacity in such settings.

Phenotypic low-level isoniazid resistance as a marker to predict ethionamide resistance in Mycobacterium tuberculosis.

BACKGROUND: Tuberculosis is one of the most prevalent diseases in Pakistan. Pakistan has the highest burden of MDR-TB in the Eastern Mediterranean region. Ethionamide is an anti-tuberculous drug frequently used to treat MDR-TB. Its drug susceptibility testing is not easily available in resource limited settings. Since it acts on the same target protein as isoniazid (inhA protein encoded by inhA gene), we sought to find out if phenotypic isoniazid resistance can be a marker of ethionamide resistance. MATERIALS AND METHODS: This was a retrospective observational study conducted at the Aga Khan University hospital section of microbiology. Data was retrieved between 2011 to 2014 for all culture positive MTB strains. All culture positive MTB isolates with susceptibilities to isoniazid and ethionamide recorded were included in the study. Isoniazid and ethionamide susceptibilities were performed using agar proportion method on Middlebrook 7H10 agar. Rate of Ethionamide resistance between low-level isoniazid resistant, high level isoniazid resistant and isoniazid sensitive MTB was compared. RESULTS: A total of 11,274 isolates were included in the study. A statistically significant association (P < 0.001) was found between Ethionamide resistance and low-level isoniazid resistance (26.6%) as compared to high-level isoniazid resistance (8.85%) and isoniazid sensitivity (0.71%) in MTB strains. However this association was not seen in XDR-TB strains. CONCLUSION: Low level isoniazid resistance may be used as marker for phenotypic ethionamide resistance and hence guide clinicians' choice of antituberculous agent for MDR-TB in Pakistan. Further studies involving detection of genotypic association of isoniazid and ethionamide susceptibilities are needed before a final conclusion can be derived.

Fluoroquinolone resistance in Mycobacterium tuberculosis isolates from Pakistan 2010-2014: Implications for disease control.

INTRODUCTION: Fluoroquinolones (FQ) are an essential component of current and new regimens for the treatment of tuberculosis (TB). The 2014 Global TB report indicates a FQ resistance rate of 17% amongst multidrug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB) tested in 2013. There is, however, a paucity of FQ-resistance data from high burden countries. In this study the trend of FQ-resistance amongst MDR-MTB and non-MDR-MTB is analyzed over a four-and-a-half-year period (January 2010-July 2014). METHODS: This study was conducted at the Aga Khan University laboratory, a technical partner of the Pakistan National TB Program and part of the World Health Organization (WHO) Supra-national Laboratory Network for TB. The laboratory receives specimens from across the country through its peripheral collection units. MTB was isolated using standard methods. Susceptibility testing was performed using the agar proportion method with drug concentrations as recommended by Clinical Laboratory Institute Standards (CLSI). FQ susceptibilities were determined using ofloxacin (2µg/ml). MTB H37Rv was used as a control with each batch of susceptibility testing. MDR was defined as resistance to both isoniazid (0.2µg/ml) and rifampicin (1.0µg/ml). RESULTS: During the study period 14,711 MTB strains were isolated. Of these, 6403 (43.5%) were MDR and 8308 were non-MDR. FQ resistance in MDR strains ranged between 54% and 58%. Amongst non-MDR MTB strains, FQ resistance increased from 214/2059 (10.3%) in 2010 to 180/1049 (17.1%) in 2014. The proportion of FQ mono-resistant TB strains averaged at 10.5% of the non-MDR isolates during this period. CONCLUSIONS: FQ resistance in non-MDR-MTB strains with a considerable proportion of FQ mono-resistant strains in Pakistan is alarming. These data highlight the limited potential of empirical FQ usage for TB treatment in both MDR and non-MDR cases and the need to implement regular surveillance for FQ-resistance in MTB in the country. High FQ resistance amongst MTB isolates further emphasizes the importance of stewardship and the responsible use of FQs in particular, and antimicrobials in general in the country.

Antimicrobial resistance in Salmonella enterica serovar typhi and paratyphi in South Asia-current status, issues and prospects.

The human race owes a debt of gratitude to antimicrobial agents, penicillin and its successors that have saved people from tremendous pain and suffering in the last several decades. Unfortunately, this consideration is no more true, as millions of people are prone to the challenging threat of emergence of antimicrobial resistance worldwide and the menace is more distressing in developing countries. Comparable with other bacterial species, Salmonella enterica serovar Typhi (S. typhi) and Paratyphi (S. paratyphi) have been evolving multidrug resistance (MDR) against a wide array of antibiotics, including chloramphenicol, ampicillin and co-trimoxazole, and globally affecting 21 million people with 220,000 deaths each year. S. typhi and S. paratyphi infections are also endemic in South Asia and a series of antibiotics used to treat these infections, have been losing efficacy against enteric fever. Currently, quinolones are regarded as a choice to treat MDR Salmonella in these regions. Travel-related cases of enteric fever, especially from South Asian countries are the harbinger of the magnitude of MDR Salmonella in that region. Conclusively, the MDR will continue to grow and the available antimicrobial agents would become obsolete. Therefore, a radical and aggressive approach in terms of rational use of antibiotics during treating infections is essentially needed.

Antimicrobial susceptibility and genetic characteristics of Neisseria gonorrhoeae isolates from India, Pakistan and Bhutan in 2007-2011.

BACKGROUND: Knowledge on antimicrobial drug resistance and genetic characteristics of Neisseria gonorrhoeae isolates circulating in India, Pakistan, and Bhutan is sorely lacking. In this paper, we describe the prevalence of antimicrobial resistance and molecular characteristics of N. gonorrhoeae isolates from India, Pakistan, and Bhutan in 2007-2011. METHODS: Antimicrobial susceptibility and ß-lactamase production were tested for 65 N. gonorrhoeae isolates from India (n=40), Pakistan (n=18) and Bhutan (n=7) using Etest methodology (eight antimicrobials) and nitrocefin solution, respectively. Resistance determinants, i.e. penA, mtrR, porB1b, gyrA, and parC, were sequenced. N. gonorrhoeae multiantigen sequence typing (NG-MAST) was performed for molecular epidemiology. RESULTS: The highest resistance level was observed for ciprofloxacin (94%), followed by penicillin G (68%), erythromycin (62%), tetracycline (55%), and azithromycin (7.7%). All the isolates were susceptible to ceftriaxone, cefixime, and spectinomycin. Thirty-four (52%) of the isolates were producing ß-lactamase. No penA mosaic alleles or A501-altered alleles of penicillin-binding protein 2 were identified. Forty-nine NG-MAST STs were identified, of which 42 STs have not been previously described worldwide. CONCLUSIONS: Based on this study, ceftriaxone, cefixime, and spectinomycin can be used as an empirical first-line therapy for gonorrhoea in India, Pakistan, and Bhutan, whereas ciprofloxacin, penicillin G, tetracycline, erythromycin, and azithromycin should not be. It is imperative to strengthen the laboratory infrastructure in this region, as well as to expand the phenotypic and genetic surveillance of antimicrobial resistance, emergence of new resistance, particularly, to extended-spectrum cephalosporins, and molecular epidemiology.

High isoniazid resistance rates in rifampicin susceptible Mycobacterium tuberculosis pulmonary isolates from Pakistan.

BACKGROUND: Rapid new diagnostic methods (including Xpert MTB/RIF assay) use rifampicin resistance as a surrogate marker for multidrug resistant tuberculosis. Patients infected with rifampicin susceptible strains are prescribed first line anti-tuberculosis therapy. The roll out of such methods raises a concern that strains with resistance to other first line anti-tuberculosis drugs including isoniazid will be missed and inappropriate treatment given. To evaluate implications of using such methods review of resistance data from high burden settings such as ours is essential. OBJECTIVE: To determine resistance to first line anti-tuberculosis drugs amongst rifampicin susceptible pulmonary Mycobacterium tuberculosis (MTB) isolates from Pakistan. MATERIALS AND METHODS: Data of pulmonary Mycobacterium tuberculosis strains isolated in Aga Khan University Hospital (AKUH) laboratory (2009-2011) was retrospectively analyzed. Antimicrobial susceptibility profile of rifampicin susceptible isolates was evaluated for resistance to isoniazid, pyrazinamide, ethambutol, and streptomycin. RESULTS: Pulmonary specimens submitted to AKUH from 2009 to 2011 yielded 7738 strains of Mycobacterium tuberculosis. These included 54% (n 4183) rifampicin susceptible and 46% (n: 3555) rifampicin resistant strains. Analysis of rifampicin susceptible strains showed resistance to at least one of the first line drugs in 27% (n:1133) of isolates. Overall isoniazid resistance was 15.5% (n: 649), with an isoniazid mono-resistance rate of 4% (n: 174). Combined resistance to isoniazid, pyrazinamide, and ethambutol was noted in 1% (n: 40), while resistance to isoniazid, pyrazinamide, ethambutol, and streptomycin was observed in 1.7% (n: 70) of strains. CONCLUSIONS: Our data suggests that techniques (including Xpert MTB/RIF assay) relying on rifampicin susceptibility as an indicator for initiating first line therapy will not detect patients infected with MTB strains resistant to other first line drugs (including isoniazid). The roll out of these techniques must therefore be accompanied by strict monitoring ensuring early resistance detection to increase chances of improved patient outcomes.