Balancing science and public policy in Pakistan\u27s COVID-19 response

Background: Coronavirus disease 2019 (COVID-19) has affected the world in an unprecedented manner and South Asian countries were among the first to experience imported cases. Pakistan\u27s response to COVID-19 has been under scrutiny for its granularity, reach and impact.Aims: to evaluate objectively the chronology and depth of the response to COVID-19 in Pakistan.Methods: We evaluated available national and subnational epidemiological and burden information on COVID-19 cases and deaths in Pakistan, including projection models available to the Government at an early stage of the pandemic.Results: Pakistan, with a population of 215 million and considerable geographic diversity, experienced case introduction from pilgrims returning from the Islamic Republic of Iran, followed by widespread community transmission. The National Command and Operations Centre, established through civilian and military partnership, was critical in fast tracking logistics, information gathering, real-time reporting and smart lockdowns, coupled with a massive cash support programme targeting the poorest sections of society. Cases peaked in June 2020 but the health system was able to cope with the excess workload. Since then, although testing rates remain low (\u3e 300 000 cases confirmed to date), case fatality rates have stabilized, and with 6300 deaths, Pakistan seems to have flattened the COVID-19 curve.Conclusion: Despite notable successes in controlling the pandemic, several weaknesses remain and there are risks of rebound as the economy and educational systems reopen. There is continued need for strong technical and programmatic oversight, linked to civic society engagement and working with religious scholars to ensure nonpharmacological intervention compliance

Balancing science and public policy in Pakistan\u27s COVID-19 response

Background: Coronavirus disease 2019 (COVID-19) has affected the world in an unprecedented manner and South Asian countries were among the first to experience imported cases. Pakistan\u27s response to COVID-19 has been under scrutiny for its granularity, reach and impact.Aims: to evaluate objectively the chronology and depth of the response to COVID-19 in Pakistan.Methods: We evaluated available national and subnational epidemiological and burden information on COVID-19 cases and deaths in Pakistan, including projection models available to the Government at an early stage of the pandemic.Results: Pakistan, with a population of 215 million and considerable geographic diversity, experienced case introduction from pilgrims returning from the Islamic Republic of Iran, followed by widespread community transmission. The National Command and Operations Centre, established through civilian and military partnership, was critical in fast tracking logistics, information gathering, real-time reporting and smart lockdowns, coupled with a massive cash support programme targeting the poorest sections of society. Cases peaked in June 2020 but the health system was able to cope with the excess workload. Since then, although testing rates remain low (\u3e 300 000 cases confirmed to date), case fatality rates have stabilized, and with 6300 deaths, Pakistan seems to have flattened the COVID-19 curve.Conclusion: Despite notable successes in controlling the pandemic, several weaknesses remain and there are risks of rebound as the economy and educational systems reopen. There is continued need for strong technical and programmatic oversight, linked to civic society engagement and working with religious scholars to ensure nonpharmacological intervention compliance

Unique Pakistani gut microbiota highlights population-specific microbiota signatures of type 2 diabetes mellitus

Biogeographic variations in the gut microbiota are pivotal to understanding the global pattern of host–microbiota interactions in prevalent lifestyle-related diseases. Pakistani adults, having an exceptionally high prevalence of type 2 diabetes mellitus (T2D), are one of the most understudied populations in microbiota research to date. The aim of the present study is to examine the gut microbiota across individuals from Pakistan and other populations of non-industrialized and industrialized lifestyles with a focus on T2D. The fecal samples from 94 urban-dwelling Pakistani adults with and without T2D were profiled by bacterial 16S ribosomal RNA gene and fungal internal transcribed spacer (ITS) region amplicon sequencing and eubacterial qPCR, and plasma samples quantified for circulating levels of lipopolysaccharide-binding protein (LBP) and the activation ability of Toll-like receptor (TLR)-signaling. Publicly available datasets generated with comparable molecular methods were retrieved for comparative analysis of the bacterial microbiota. Overall, urbanized Pakistanis’ gut microbiota was similar to that of transitional or non-industrialized populations, depleted in Akkermansiaceae and enriched in Prevotellaceae (dominated by the non-Westernized clades of Prevotella copri). The relatively high proportion of Atopobiaceae appeared to be a unique characteristic of the Pakistani gut microbiota. The Pakistanis with T2D had elevated levels of LBP and TLR-signaling in circulation as well as gut microbial signatures atypical of other populations, e.g., increased relative abundance of Libanicoccus/Parolsenella, limiting the inter-population extrapolation of gut microbiota-based classifiers for T2D. Taken together, our findings call for a more global representation of understudied populations to extend the applicability of microbiota-based diagnostics and therapeutics.Peer reviewe

Emergence of resistance to fluoroquinolones and third-generation cephalosporins in Salmonella Typhi in Lahore, Pakistan

Extensively drug-resistant (XDR) Salmonella Typhi has been reported in Sindh province of Pakistan since 2016. The potential for further spread is of serious concern as remaining treatment options are severely limited. We report the phenotypic and genotypic characterization of 27 XDR S. Typhi isolated from patients attending Jinnah Hospital, Lahore, Pakistan. Isolates were identified by biochemical profiling; antimicrobial susceptibility was determined by a modified Kirby-Bauer method. These findings were confirmed using Illumina whole genome nucleotide sequence data. All sequences were compared to the outbreak strain from Southern Pakistan and typed using the S. Typhi genotyping scheme. All isolates were confirmed by a sequence analysis to harbor an IncY plasmid and the CTX-M-15 ceftriaxone resistance determinant. All isolates were of the same genotypic background as the outbreak strain from Sindh province. We report the first emergence of XDR S. Typhi in Punjab province of Pakistan confirmed by whole genome sequencing

Using critical information to strengthen pandemic preparedness: the role of national public health agencies.

COVID-19 has demonstrated that most countries' public health systems and capacities are insufficiently prepared to prevent a localised infectious disease outbreak from spreading. Strengthening national preparedness requires National Public Health Institutes (NPHIs), or their equivalent, to overcome practical challenges affecting timely access to, and use of, data that is critical to preparedness. Our situational analysis in collaboration with NPHIs in three countries-Ethiopia, Nigeria and Pakistan-characterises these challenges. Our findings indicate that NPHIs' role necessitates collection and analysis of data from multiple sources that do not routinely share data with public health authorities. Since initiating requests for access to new data sources can be a lengthy process, it is essential that NPHIs are routinely monitoring a broad set of priority indicators that are selected to reflect the country-specific context. NPHIs must also have the authority to be able to request rapid sharing of data from public and private sector organisations during health emergencies and to access additional human and financial resources during disease outbreaks. Finally, timely, transparent and informative communication of synthesised data from NPHIs will facilitate sustained data sharing with NPHIs from external organisations. These actions identified by our analysis will support the availability of robust information systems that allow relevant data to be collected, shared and analysed by NPHIs sufficiently rapidly to inform a timely local response to infectious disease outbreaks in the future

Improving National Intelligence for Public Health Preparedness: a methodological approach to finding local multi-sector indicators for health security.

The COVID-19 epidemic is the latest evidence of critical gaps in our collective ability to monitor country-level preparedness for health emergencies. The global frameworks that exist to strengthen core public health capacities lack coverage of several preparedness domains and do not provide mechanisms to interface with local intelligence. We designed and piloted a process, in collaboration with three National Public Health Institutes (NPHIs) in Ethiopia, Nigeria and Pakistan, to identify potential preparedness indicators that exist in a myriad of frameworks and tools in varying local institutions. Following a desk-based systematic search and expert consultations, indicators were extracted from existing national and subnational health security-relevant frameworks and prioritised in a multi-stakeholder two-round Delphi process. Eighty-six indicators in Ethiopia, 87 indicators in Nigeria and 51 indicators in Pakistan were assessed to be valid, relevant and feasible. From these, 14-16 indicators were prioritised in each of the three countries for consideration in monitoring and evaluation tools. Priority indicators consistently included private sector metrics, subnational capacities, availability and capacity for electronic surveillance, measures of timeliness for routine reporting, data quality scores and data related to internally displaced persons and returnees. NPHIs play an increasingly central role in health security and must have access to data needed to identify and respond rapidly to public health threats. Collecting and collating local sources of information may prove essential to addressing gaps; it is a necessary step towards improving preparedness and strengthening international health regulations compliance

Multinational prospective cohort study of rates and risk factors for ventilator-associated pneumonia over 24 years in 42 countries of Asia, Africa, Eastern Europe, Latin America, and the Middle East: Findings of the International Nosocomial Infection Control Consortium (INICC)

Objective: Rates of ventilator-associated pneumonia (VAP) in low- and middle-income countries (LMIC) are several times above those of high-income countries. The objective of this study was to identify risk factors (RFs) for VAP cases in ICUs of LMICs. Design: Prospective cohort study. Setting: This study was conducted across 743 ICUs of 282 hospitals in 144 cities in 42 Asian, African, European, Latin American, and Middle Eastern countries. Participants: The study included patients admitted to ICUs across 24 years. Results: In total, 289,643 patients were followed during 1,951,405 patient days and acquired 8,236 VAPs. We analyzed 10 independent variables. Multiple logistic regression identified the following independent VAP RFs: male sex (adjusted odds ratio [aOR], 1.22; 95% confidence interval [CI], 1.16-1.28; P <.0001); longer length of stay (LOS), which increased the risk 7% per day (aOR, 1.07; 95% CI, 1.07-1.08; P <.0001); mechanical ventilation (MV) utilization ratio (aOR, 1.27; 95% CI, 1.23-1.31; P <.0001); continuous positive airway pressure (CPAP), which was associated with the highest risk (aOR, 13.38; 95% CI, 11.57-15.48; P <.0001)Revisión por pare

An international prospective study of INICC analyzing the incidence and risk factors for catheter-associated urinary tract infections in 235 ICUs across 8 Asian Countries

Background: Identify urinary catheter (UC)-associated urinary tract infections (CAUTI) incidence and risk factors (RF) in 235 ICUs in 8 Asian countries: India, Malaysia, Mongolia, Nepal, Pakistan, the Philippines, Thailand, and Vietnam. Methods: From January 1, 2014, to February 12, 2022, we conducted a prospective cohort study. To estimate CAUTI incidence, the number of UC days was the denominator, and CAUTI was the numerator. To estimate CAUTI RFs, we analyzed 11 variables using multiple logistic regression. Results: 84,920 patients hospitalized for 499,272 patient days acquired 869 CAUTIs. The pooled CAUTI rate per 1,000 UC-days was 3.08; for those using suprapubic-catheters (4.11); indwelling-catheters (2.65); trauma-ICU (10.55), neurologic-ICU (7.17), neurosurgical-ICU (5.28); in lower- middle-income countries (3.05); in upper-middle-income countries (1.71); at public-hospitals (5.98), at private-hospitals (3.09), at teaching-hospitals (2.04). The following variables were identified as CAUTI RFs: Age (adjusted odds ratio [aOR] = 1.01; 95% CI = 1.01-1.02; P < .0001); female sex (aOR = 1.39; 95% CI = 1.21-1.59; P < .0001); using suprapubic-catheter (aOR = 4.72; 95% CI = 1.69-13.21; P < .0001); length of stay before CAUTI acquisition (aOR = 1.04; 95% CI = 1.04-1.05; P < .0001); UC and device utilization-ratio (aOR = 1.07; 95% CI = 1.01-1.13; P = .02); hospitalized at trauma-ICU (aOR = 14.12; 95% CI = 4.68-42.67; P < .0001), neurologic-ICU (aOR = 14.13; 95% CI = 6.63-30.11; P < .0001), neurosurgical-ICU (aOR = 13.79; 95% CI = 6.88-27.64; P < .0001); public-facilities (aOR = 3.23; 95% CI = 2.34-4.46; P < .0001). Discussion: CAUTI rate and risk are higher for older patients, women, hospitalized at trauma-ICU, neurologic-ICU, neurosurgical-ICU, and public facilities. All of them are unlikely to change. Conclusions: It is suggested to focus on reducing the length of stay and the Urinary catheter device utilization ratio, avoiding suprapubic catheters, and implementing evidence-based CAUTI prevention recommendations