Covid-19 related isolation and risk of post-traumatic stress disorder in patients presenting to tele-clinics at a private tertiary care hospital in Karachi

The objective of this study was to assess the psychological impact of isolation on individuals with Covid-19 and determine the experiences of people in isolation. All adults with Covid-19 who reported to the infectious disease tele-clinic were included in the study; participants were sent the survey form via email. The email was sent to 146 people and 47 responses were received. IES-R questionnaire was submitted to all individuals on Day 7 of quarantine, along with a qualitative questionnaire. The mean score on IES-R for all the respondents was 18.77. Out of 47 participants, for 6 (12.8%) PTSD was a clinical concern, 3 (6.4%) participants had a probable diagnosis of PTSD, and 6 (12.8%) participants scored high enough to suppress immune function. The majority of participants reported stress due to confinement in an isolated space and interruption in daily routine, specifically work-related routine. Praying, meditation, and having social support helped the participants cope with the isolation.

Exploring the relationship between SARS-CoV-2 variants, illness severity at presentation, in-hospital mortality and COVID-19 vaccination in a low middle-income country: A retrospective cross-sectional study

Background and Aims

COVID-19 morbidity and mortality varied globally through the pandemic. We studied the relationship of SARS-CoV-2 variants of concern (VOC) with COVID-19 severity and mortality among hospitalized patients in Pakistan.

Methods

A retrospective review of clinical, laboratory, and vaccination data of 197 COVID-19 adult patients at the Aga Khan University Hospital, Karachi between April 2021, and February 2022 was performed. SARS-CoV-2 VOC identified in respiratory samples were analyzed. Univariate and multivariate analysis was conducted to identify factors associated with COVID-19 outcomes.

Results

The median age of cases was 55 years and 51.8% were males. Twenty-four percent of females were pregnant. Of COVID-19 cases, 48.2% had nonsevere disease, while 52.8% had severe/critical disease. Hypertension (48%) and diabetes mellitus (41%) were common comorbids. SARS-CoV-2 VOC identified comprised; Omicron (55.3%), Beta (14.7%), Alpha (13.7%), Delta (12.7%), and Gamma (3.6%) variants. Most (59.7%) study subjects were unvaccinated. Of vaccines, 88% had received inactivated virus COVID-19 vaccines. Increased risk of severe disease was associated with age ≥50 years (odds ratio [OR]: 5.73; 95% confidence interval [CI]: [2.45-13.7]), as well as with diabetes mellitus (OR: 4.24; 95% CI: [1.82-9.85]). Full vaccination (OR: 0.25; 95% CI: [0.11-0.58]) or infection with Omicron (OR: 0.42; 95% CI: [0.23-0.74]) was associated with reduced disease severity. The risk of mortality increased with age ≥50 years (OR: 5.07; 95% CI: [1.92-13.42]) and a history of myocardial infarction (OR: 5.11; 95% CI: [1.45-17.93]) whilst, infection with Omicron was found to reduce the risk (OR: 0.22; 95% CI: [0.10-0.53]).

Conclusion

Our study describes the relationship between the severity of COVID-19, in-hospital mortality in relation to SARS-CoV-2 variants, and the impact of COVID-19 vaccination in Pakistan. Outcomes were more favorable in younger individuals, after vaccinations and with Omicron variant infections. Most cases received inactivated virus vaccines therefore these data highlight the protection provided against severe COVID-19.

Humoral and T cell responses to SARS-CoV-2 reveal insights into immunity during the early pandemic period in Pakistan

BACKGROUND

Protection against SARS-CoV-2 is mediated by humoral and T cell responses. Pakistan faced relatively low morbidity and mortality from COVID-19 through the pandemic. To examine the role of prior immunity in the population, we studied IgG antibody response levels, virus neutralizing activity and T cell reactivity to Spike protein in a healthy control group (HG) as compared with COVID-19 cases and individuals from the pre-pandemic period (PP).

METHODS

HG and COVID-19 participants were recruited between October 2020 and May 2021. Pre-pandemic sera was collected before 2018. IgG antibodies against Spike and its Receptor Binding Domain (RBD) were determined by ELISA. Virus neutralization activity was determined using a PCR-based micro-neutralization assay. T cell - IFN-γ activation was assessed by ELISpot.

RESULTS

Overall, the magnitude of anti-Spike IgG antibody levels as well as seropositivity was greatest in COVID-19 cases (90%) as compared with HG (39.8%) and PP (12.2%). During the study period, Pakistan experienced three COVID-19 waves. We observed that IgG seropositivity to Spike in HG increased from 10.3 to 83.5% during the study, whilst seropositivity to RBD increased from 7.5 to 33.3%. IgG antibodies to Spike and RBD were correlated positively in all three study groups. Virus neutralizing activity was identified in sera of COVID-19, HG and PP. Spike reactive T cells were present in COVID-19, HG and PP groups. Individuals with reactive T cells included those with and without IgG antibodies to Spike.

CONCLUSIONS

Antibody and T cell responses to Spike protein in individuals from the pre-pandemic period suggest prior immunity against SARS-CoV-2, most likely from cross-reactive responses. The rising seroprevalence observed in healthy individuals through the pandemic without known COVID-19 may be due to the activation of adaptive immunity from cross-reactive memory B and T cells. This may explain the more favourable COVID-19 outcomes observed in this population.

Impact of Postoperative Antibiotic Prophylaxis on Surgical Site Infections Rates After Mastectomy with Drains but Without Immediate Reconstruction: A Multicenter, Double-Blinded, Randomized Control Superiority Trial

BACKGROUND

There is no consensus on the use of postoperative antibiotic prophylaxis (PAP) after mastectomy with indwelling drains. We explored the utility of continued PAP in reducing surgical site infection (SSI) rates after mastectomy without immediate reconstruction and with indwelling drains.

PATIENTS AND METHODS

A multicenter, two-armed, randomized control superiority trial was conducted in Pakistan. We enrolled all consenting adult patients undergoing mastectomy without immediate reconstruction. All patients received a single preoperative dose of cephalexin within 60 min of incision, and postoperatively were randomized to receive either continued PAP using cephalexin (intervention) or a placebo (control) for the duration of indwelling, closed-suction drains. The primary outcome was the development of SSI within 30 days and 90 days postoperatively. Secondary outcomes included study-drug-associated adverse events. Intention-to-treat analysis was performed using multivariable Cox regression.

RESULTS

A total of 369 patients, 180 (48.8%) in the intervention group and 189 (51.2%) in the control group, were included in the final analysis. Overall cumulative SSI rates were 3.5% at 30 days and 4.6% at 90 days postoperatively. PAP was not associated with SSI reduction at 30 (hazard ratio, HR 1.666 [95% confidence interval CI 0.515-5.385]) or 90 (1.575 [0.558-4.448]) days postoperatively, or with study-drug-associated adverse effects (0.529 [0.196-1.428]).

CONCLUSIONS

Continuing antibiotic prophylaxis for the duration of indwelling drains after mastectomy without immediate reconstruction offers no additional benefit in terms of SSI reduction. There is a need to update existing guidelines to provide clearer recommendations regarding use of postoperative antibiotic prophylaxis after mastectomy in the setting of indwelling drains.

Investigating the impact of prior COVID-19 on IgG antibody and interferon γ responses after BBIBP-CorV vaccination in a disease endemic population: A prospective observational study

Background and Aims

COVID-19 vaccinations have reduced morbidity and mortality from the disease. Antibodies against severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) have been associated with immune protection. Seroprevalence studies revealed high immunoglobulin G (IgG) antibody levels to SARS-CoV-2 in the Pakistani population before vaccinations. We investigated the effect of BBIBP-CorV vaccination on circulating IgG antibodies and interferon (IFN)-γ from T cells measured in a cohort of healthy individuals, with respect to age, gender, and history of COVID-19.

Methods

The study was conducted between April and October 2021. BBIBP-CorV vaccinated participants were followed up to 24 weeks. Antibodies to SARS-CoV-2 Spike protein and its receptor-binding domain (RBD) were measured. IFNγ secreted by whole blood stimulation of Spike protein and extended genome antigens was determined.

Results

Study participants with a history of prior COVID-19 displayed a higher magnitude of IgG antibodies to Spike and RBD. IgG seropositivity was greater in those with prior COVID-19, aged 50 years or younger and in females. At 24 weeks after vaccination, 37.4% of participants showed IFN-γ responses to SARS-CoV-2 antigens. T cell IFN-γ release was higher in those with prior COVID-19 and those aged 50 years or less. Highest IFN-γ release was observed to extended genome antigens in individuals both with and without prior COVID-19.

Conclusion

We found that IgG seropositivity to both Spike and RBD was affected by prior COVID-19, age and gender. Importantly, seropositive responses persisted up to 24 weeks after vaccination. Persistence of vaccine induced IgG antibodies may be linked to the high seroprevalence observed earlier in unvaccinated individuals. Increased T cell reactivity to Spike and extended genome antigens reflects cellular activation induced by BBIBP-CorV. COVID-19 vaccination may have longer lasting immune responses in populations with a higher seroprevalence. These data inform on vaccination booster policies for high-risk groups.

Genetic and antiretroviral drug resistance mutations analysis of reverse transcriptase and protease gene from Pakistani people living with HIV-1

BACKGROUND

Antiretroviral therapy (ART) effectiveness is compromised by the emergence of HIV drug resistance mutations (DRM) and can lead to the failure of ART. Apart from intrinsic viral factors, non-compliance with drugs and/or the use of sub-optimum therapy can lead to the emergence of DRMs. In Pakistan HIV currently exists as a concentrated epidemic, however, ART coverage is very low, and drug adherence is poor. ART is selected assuming without baseline genotyping. Pakistan has recently seen a rise in treatment failures, but the country's actual burden of DRM is still unknown. In this study, we perform the genetic and drug resistance analysis of the pol gene from Pakistani HIV-positive ART-naïve and ART-experienced individuals.

METHODS

In this study, HIV-1 pol was sequenced from 146 HIV-1 positive individuals, divided into ART-naïve (n = 37) and ART-experienced (n = 109). The sequences were also used to determine HIV-1 subtypes, the prevalence of DRM, and pol genetic variability.

RESULTS

DRM analysis identified numerous DRMs against reverse transcriptase inhibitors in both ART-naïve and ART-experienced groups, including a few that are classified as rare. Additionally, the ART-experienced group showed mutations associated with resistance to protease inhibitors. Genetic analysis showed negative selection pressure in both groups, but a higher rate of evolution in the ART-naïve group.

CONCLUSION

High prevalence of DRMs, especially against previous first-line treatment in ART- naïve and the accumulation of DRMs in ART-experienced groups is concerning and warrants that a more extensive DRM survey be carried out to inform first-line and second-line ART regimen recommendations.

ACORN (A Clinically-Oriented Antimicrobial Resistance Surveillance Network) II: protocol for case based antimicrobial resistance surveillance

Background: Antimicrobial resistance surveillance is essential for empiric antibiotic prescribing, infection prevention and control policies and to drive novel antibiotic discovery. However, most existing surveillance systems are isolate-based without supporting patient-based clinical data, and not widely implemented especially in low- and middle-income countries (LMICs). Methods: A Clinically-Oriented Antimicrobial Resistance Surveillance Network (ACORN) II is a large-scale multicentre protocol which builds on the WHO Global Antimicrobial Resistance and Use Surveillance System to estimate syndromic and pathogen outcomes along with associated health economic costs. ACORN-healthcare associated infection (ACORN-HAI) is an extension study which focuses on healthcare-associated bloodstream infections and ventilator-associated pneumonia. Our main aim is to implement an efficient clinically-oriented antimicrobial resistance surveillance system, which can be incorporated as part of routine workflow in hospitals in LMICs. These surveillance systems include hospitalised patients of any age with clinically compatible acute community-acquired or healthcare-associated bacterial infection syndromes, and who were prescribed parenteral antibiotics. Diagnostic stewardship activities will be implemented to optimise microbiology culture specimen collection practices. Basic patient characteristics, clinician diagnosis, empiric treatment, infection severity and risk factors for HAI are recorded on enrolment and during 28-day follow-up. An R Shiny application can be used offline and online for merging clinical and microbiology data, and generating collated reports to inform local antibiotic stewardship and infection control policies. Discussion: ACORN II is a comprehensive antimicrobial resistance surveillance activity which advocates pragmatic implementation and prioritises improving local diagnostic and antibiotic prescribing practices through patient-centred data collection. These data can be rapidly communicated to local physicians and infection prevention and control teams. Relative ease of data collection promotes sustainability and maximises participation and scalability. With ACORN-HAI as an example, ACORN II has the capacity to accommodate extensions to investigate further specific questions of interest.

Effectiveness of inactivated COVID-19 vaccines against SARS-CoV-2 infections among healthcare personnel in Pakistan: a test-negative case-control study

OBJECTIVE

During the COVID-19 pandemic, several vaccines that were efficacious in randomised controlled trials were authorised for mass vaccination. In developing countries, inactivated vaccines were widely administered. While inactivated vaccines have been deemed effective in reducing disease severity, for healthcare personnel (HCP), effectiveness against SARS-CoV-2 infections is essential to reduce the risk to vulnerable patients and ensure a stable healthcare workforce. There are limited studies examining inactivated vaccines' effectiveness against SARS-CoV-2 variants of concern (VOCs) in real-world settings. We estimated the effectiveness of inactivated vaccines (BBIBP-CorV and CoronaVac) against reverse transcription PCR (RT-PCR)-confirmed SARS-CoV-2 infections among HCP in the setting of emerging SARS-CoV-2 VOCs in Pakistan.

DESIGN

A retrospective matched, test-negative case-control analysis using existing data from an Employee Health database on HCP at a large, private healthcare system in Pakistan.

PARTICIPANTS

4599 HCP were tested between 1 April and 30 September 2021. Each case (PCR positive) was matched to two to six controls (PCR negative) by the date of the RT-PCR test (±7 days) to reduce bias.

PRIMARY AND SECONDARY OUTCOME MEASURES

The primary outcome was vaccine effectiveness (VE) against SARS-CoV-2 infection. The secondary outcome was VE against symptomatic SARS-CoV-2 infection. Per cent VE was calculated using (1-OR)*100, with the OR of getting a PCR-confirmed SARS-COV-2 infection estimated using conditional logistic regression, after adjusting for age, gender, work area and history of SARS-CoV-2 infection.

RESULTS

Inactivated vaccines were ineffective against SARS-CoV-2 infections after receiving the first dose (VE 17%, 95% CI -10, 39; p=0.261). They showed modest effectiveness ≥14 days after the second dose against SARS-CoV-2 infections (VE 30%, 95% CI 7, 48; p=0.015) and symptomatic SARS-CoV-2 infections (VE 33%, 95% CI 6, 52; p=0.002).

CONCLUSIONS

Inactivated vaccines show modest effectiveness against SARS-CoV-2 infections in the setting of emerging VOCs. This builds a strong case for boosters and/or additional vaccination.

Tracking SARS-CoV-2 variants through pandemic waves using RT-PCR testing in low-resource settings

COVID-19 resulted in extensive morbidity and mortality worldwide. SARS-CoV-2 evolved rapidly, with increasing transmission due to Variants of Concern (VOC). Identifying VOC became important but genome submissions from low-middle income countries (LMIC) remained low leading to gaps in genomic epidemiology. We demonstrate the use of a specific mutation RT-PCR based approach to identify VOC in SARS-CoV-2 positive samples through the pandemic in Pakistan. We selected 2150 SARS-CoV-2 PCR positive respiratory specimens tested between April 2021 and February 2022, at the Aga Khan University Hospital Clinical Laboratories, Karachi, Pakistan. Commercially available RT-PCR assays were used as required for mutations in Spike protein (N501Y, A570D, E484K, K417N, L452R, P681R and deletion69_70) to identify Alpha, Beta, Gamma, Delta, and Omicron variants respectively. Three pandemic waves associated with Alpha, Delta and Omicron occurred during the study period. Of the samples screened, VOC were identified in 81.7% of cases comprising mainly; Delta (37.2%), Alpha (29.8%) and Omicron (17.1%) variants. During 2021, Alpha variants were predominant in April and May; Beta and Gamma variants emerged in May and peaked in June; the Delta variant peaked in July and remained predominant until November. Omicron (BA.1) emerged in December 2021 and remained predominant until February 2022. The CT values of Alpha, Beta, Gamma and Delta were all significantly higher than that of Omicron variants (p<0.0001). We observed VOC through the pandemic waves using spike mutation specific RT-PCR assays. We show the spike mutation specific RT-PCR assay is a rapid, low-cost and adaptable for the identification of VOC as an adjunct approach to NGS to effectively inform the public health response. Further, by associating the VOC with CT values of its diagnostic PCR we gain information regarding the viral load of samples and therefore the level of transmission and disease severity in the population.

Using rapid antigen testing for early, safe return-to-work for healthcare personnel after SARS-CoV-2 infection in a healthcare system in Pakistan: A retrospective cross-sectional study

Anticipating staff shortage during the Omicron variant surge, we modified the US Centers for Disease Control and Prevention's contingency guidelines at a healthcare system in Pakistan. Infected staff had a SARS-CoV-2 rapid antigen test after 5-7 days of isolation, to decide a safe return-to-work. This led to signifcant cost savings without compromising patient/staff safety.

VITT with inactivated SARS-CoV-2 vaccine - index case

We report a case of vaccine-induced immune thrombotic thrombocytopenia (VITT) in a 73-year-old gentleman who presented with pulmonary embolism and thrombocytopenia, two weeks after receiving inactivated COVID-19 vaccine. He responded well to nonheparin anticoagulation with complete resolution of symptoms and platelet count.

Extended drug-resistant Salmonella typhi osteomyelitis: a case report and literature review

Background

Salmonella typhi infection commonly results in gastroenteritis, bacteremia with or without secondary seeding, or asymptomatic carrier stage. Few cases of Salmonella typhi bacteremia later result in seeding and ultimately lead to further complications including osteomyelitis and rarely vertebral osteomyelitis.

Case presentation

We are discussing a case of a 38-year-old Asian male patient, with no known comorbids. He presented with fever and backache for 4 weeks. Based on the magnetic resonance imaging (MRI) findings of the spine and positive blood cultures, a diagnosis of XDR Salmonella typhi (S. typhi) osteomyelitis (OM) was made. Patient was started on intravenous therapy as per culture report which was later modified according to treatment response.

Conclusion

S. typhi has a broad spectrum of clinical manifestations including osteomyelitis however to the best of our knowledge this is the first reported case of XDR S. typhi vertebral osteomyelitis. We describe the clinical course of the patient and review the literature regarding the treatment of S.typhi vertebral osteomyelitis with a special focus on XDR S. typhi. Treatment course and complications in view of this new resistant strain have to be reported in order to devise general guidelines for the management in such particular cases.

Phylogenetic and drug- and vaccine-resistance profiles of Hepatitis B Virus among children with HIV co-infection in Pakistan

INTRODUCTION

HIV-1 and hepatitis B virus (HBV) share common routes of transmission and therefore co-infection is common. In 2019, an HIV-1 outbreak that resulted in >1000 children being infected, predominantly through nosocomial transmission, occurred in Sindh, Pakistan. We conducted a phylogenetic and drug resistance analysis of the HBV Reverse Transcriptase (RT) gene in children with HIV-1 and HBV co-infection.

METHODOLOGY

Blood samples were collected from 321 children with HIV who were recruited as part of a study to investigate the HIV-1 outbreak. All samples were tested for HBV surface antigen (HBsAg) using an ELISA assay, and positive samples were used to amplify and sequence the HBV RT gene. The phylogenetic relationship between sequences was analyzed, and drug- and vaccine- resistance mutations in the RT gene were explored.

RESULTS

Of 321 samples, 23% (n = 75) were positive for HBsAg on ELISA. Phylogenetic analysis of the sequences revealed that 63.5% of HBV sequences were sub-genotype D1, while the rest were sub-genotype D2. Cluster analysis revealed grouping of sub-genotype D1 sequences exclusively with Pakistani sequences, while clustering of sub-genotypes D2 predominantly with global sequences. The 236Y mutation associated with resistance to tenofovir was observed in 2.8% of HBV sequences. Additionally, seven vaccine escape mutations were observed, the most common being 128 V.

CONCLUSION

Our study suggests ongoing transmission of HBV D1 and D2 sub-genotypes in the HIV-1 co-infected population, likely nosocomially, given common routes of HVB and HIV-1 transmission. The prevalence of major HBV drug- and vaccine-resistant mutations remains low. Surveillance for further transmissions and the possible emergence of major drug- or vaccine-resistant variants is required.

Unassigned Complex Unique Recombinant Forms Related to CRF36_cpx in Children Identified in an HIV-1 Outbreak in Pakistan

In 2019, an outbreak of HIV infection predominantly affecting children occurred in Larkana district, Pakistan. This is the largest outbreak ever reported in this age group in Pakistan. In this study, we report two HIV-1 unique recombinant forms identified during the outbreak. Blood samples were collected from HIV-positive children as part of a case-control study to investigate the outbreak. The pol gene was sequenced and used to detect HIV subtype/recombinant forms using subtype, recombination, and phylogenetic analyses. Drug resistance mutation (DRM) analysis was performed to characterize the DRMs in each sequence. We observed the emergence of two unassigned unique recombinant forms related to CRF36_cpx in 15 individuals of the 344 samples collected. Genotype analysis revealed the presence of multiple DRMs associated with resistance to reverse transcriptase inhibitors. The discovery of these unassigned unique recombinant forms in our population highlights the need for comprehensive molecular epidemiological studies to fully understand the distribution and drug resistance patterns to aid control efforts.

Comparison of risk factors and outcome of patients with and without COVID ‐19 associated pulmonary aspergillosis from Pakistan: A case‐control study

Background

Early identification of COVID‐19‐associated pulmonary aspergillosis (CAPA) is particularly challenging in low‐ middle‐income countries where diagnostic capabilities are limited, and risk factors for CAPA have not been identified. It is also essential to recognise CAPA patients who are likely to have a poorer outcome to decide on aggressive management approaches. Therefore, this study aimed to identify risk factors and outcomes for CAPA among admitted moderate to critical COVID‐19 patients at our centre in Pakistan.

Methods

An unmatched case–control study with ratio of 1:2 was conducted on hospitalised adult patients with COVID‐19 from March 2020–July 2021. Cases were defined according to European Confederation of Medical Mycology and the International Society for Human and Animal Mycology consensus criteria. Controls were defined as patients hospitalised with moderate, severe or critical COVID‐19 without CAPA.

Results

A total of 100 CAPA cases (27 probable CAPA; 73 possible CAPA) were compared with 237 controls. Critical disease at presentation (aOR 5.04; 95% CI 2.18–11.63), age ≥ 60 years (aOR 2.00; 95% CI 1.20–3.35) and underlying co‐morbid of chronic kidney disease (CKD) (aOR 3.78; 95% CI 1.57–9.08) were identified as risk factors for CAPA. Patients with CAPA had a significantly greater proportion of complications and longer length of hospital stay (p‐value < .001). Mortality was higher in patients with CAPA (48%) as compared to those without CAPA (13.5%) [OR = 6.36(95% CI 3.6–11)].

Conclusions

CAPA was significantly associated with advanced age, CKD and critical illness at presentation, along with a greater frequency of complications and higher mortality.

Efficacy of heterologous boosting against SARS-CoV-2 using a recombinant interferon-armed fusion protein vaccine (V-01): a randomized, double-blind and placebo-controlled phase III trial

Waning of neutralizing titres along with decline of protection efficacy after the second dose of COVID-19 vaccines was observed, including China-made inactivated vaccines. Efficacy of a heterologous boosting using one dose of a recombinant SARS-CoV-2 fusion protein vaccine (V-01) in inactivated vaccine-primed population was studied, aimed to restore the immunity. A randomized, double-blind and placebo-controlled phase III trial was conducted in healthy people aged 18 years or older in Pakistan and Malaysia. Each eligible participant received one dose of the V-01 vaccine developed by Livzon Mabpharm Inc. or placebo within the 3-6 months after the two-dose primary regimen, and was monitored for safety and efficacy. The primary endpoint was protection against confirmed symptomatic SARS-CoV-2 infection. A total of 10,218 participants were randomly assigned to receive a vaccine or placebo. Virus-neutralizing antibodies were assessed in 419 participants. A dramatic increase (11.3-fold; 128.3–1452.8) of neutralizing titres was measured in the V-01 group at 14 days after the booster. Over two months of surveillance, vaccine efficacy was 47.8% (95%CI: 22.6–64.7) according to the intention-to-treat principle. The most common adverse events were transient, mild-to-moderate pain at the injection site, fever, headache, and fatigue. Serious adverse events occurred almost equally in V-01 (0.12%) and placebo (0.16%) groups. The heterologous boosting with the V-01 vaccine was safe and efficacious, which could elicit robust humoral immunity under the epidemic of the Omicron variant.

Trial registration:ClinicalTrials.gov identifier: NCT05096832.

Evolutionary History and Introduction of SARS-CoV-2 Alpha VOC/B.1.1.7 in Pakistan Through International Travelers

SARS-CoV-2 variants continue to emerge, and their identification is important for the public health response to COVID-19. Genomic sequencing provides robust information but may not always be accessible and therefore rapid mutation-based PCR approaches can be used to identify known variants. International travelers arriving in Karachi between December 2020 and February 2021 were tested for SARS-CoV-2 by PCR. A subset of positive samples was tested for S-Gene Target Failure (SGTF) on TaqPathTM COVID-19 (Thermo Fisher Scientific) and for mutations using the GSD NovaType SARS-CoV-2 (Eurofins Technologies) assays. Sequencing was conducted on the MinION platform (Oxford Nanopore Technologies (ONT). Bayesian phylogeographic inference was performed integrating the patients’ travel history information. Of the thirty-five COVID-19 cases screened, thirteen had isolates with SGTF. The travelers transmitted infection to sixty-eight contact cases. The B.1.1.7 lineage was confirmed through sequencing and PCR. Phylogenetic analysis of sequence data available for six cases included four B.1.1.7 strains and one B.1.36 and B.1.1.212 lineage isolate, respectively. Phylogeographic modeling estimated at least three independent B.1.1.7 introductions into Karachi, Pakistan, originating from the UK. B.1.1.212 and B.1.36 were inferred to be introduced either from the UK or the travelers’ layover location. We report the introduction of SARS-CoV-2 B.1.1.7 and other lineages in Pakistan by international travelers arriving via different flight routes. This highlights SARS-CoV-2 transmission through travel, importance of testing and quarantine post-travel to prevent transmission of new strains, as well as recording detailed patients’ metadata. Such results help inform policies on restricting travel from destinations where new highly transmissible variants have emerged.

The mystery of COVID-19 reinfections: A global systematic review and meta-analysis

BACKGROUND

As the COVID-19 pandemic rages on, reports on disparities in vaccine roll out alongside COVID-19 reinfection have been emerging. We conducted a systematic review to assess the determinants and disease spectrum of COVID-19 reinfection.

MATERIALS AND METHODS

A comprehensive search covering relevant databases was conducted for observational studies reporting Polymerase Chain Reaction (PCR) confirmed infection and reinfection cases. A quality assessment tool developed by the National Institute of Health (NIH) for the assessment of case series was utilized. Meta-analyses were performed using RevMan 5.3 for pooled proportions of findings in first infection and reinfection with a 95% confidence interval (CI).

RESULTS

Eighty-one studies reporting 577 cases were included from 22 countries. The mean age of patients was 46.2 ± 18.9 years and 179 (31.0%) cases of comorbidities were reported. The average time duration between first infection and reinfection was 63.6 ± 48.9 days. During first infection and reinfection, fever was the most common symptom (41.4% and 36.4%, respectively) whilst anti-viral therapy was the most common treatment regimen administered (44.5% and 43.0%, respectively). Comparable odds of symptomatic presentation and management were reported for the two infections. However, a higher Intensive Care Unit (ICU) admission rate was observed in reinfection compared to first infection (10 vs 3). Ten deaths were reported with respiratory failure being the most common cause of death (7/10 deaths).

CONCLUSION

Our findings support immunization practices given increased ICU admissions and mortality in reinfections. Our cohort serves as a guide for clinicians and authorities in devising an optimal strategy for controlling the pandemic. (249 words).

Upregulated type I interferon responses in asymptomatic COVID-19 infection are associated with improved clinical outcome

Understanding key host protective mechanisms against SARS-CoV-2 infection can help improve treatment modalities for COVID-19. We used a blood transcriptome approach to study biomarkers associated with differing severity of COVID-19, comparing severe and mild Symptomatic disease with Asymptomatic COVID-19 and uninfected Controls. There was suppression of antigen presentation but upregulation of inflammatory and viral mRNA translation associated pathways in Symptomatic as compared with Asymptomatic cases. In severe COVID-19, CD177 a neutrophil marker, was upregulated while interferon stimulated genes (ISGs) were downregulated. Asymptomatic COVID-19 cases displayed upregulation of ISGs and humoral response genes with downregulation of ICAM3 and TLR8. Compared across the COVID-19 disease spectrum, we found type I interferon (IFN) responses to be significantly upregulated (IFNAR2, IRF2BP1, IRF4, MAVS, SAMHD1, TRIM1), or downregulated (SOCS3, IRF2BP2, IRF2BPL) in Asymptomatic as compared with mild and severe COVID-19, with the dysregulation of an increasing number of ISGs associated with progressive disease. These data suggest that initial early responses against SARS-CoV-2 may be effectively controlled by ISGs. Therefore, we hypothesize that treatment with type I interferons in the early stage of COVID-19 may limit disease progression by limiting SARS-CoV-2 in the host.

Are doctors protected enough during COVID-19 in South Asia?

BACKGROUND

The highly contagious nature of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) places physicians in South Asia at high risk of contracting the infection. Accordingly, we conducted this study to provide an updated account of physician deaths in South Asia during the COVID-19 pandemic and to analyze and compare the different characteristics associated with physician mortality amongst the countries of the region.

METHODS

We performed a cross-sectional study by using published news reports on the websites of news agencies from 9 selected countries in South Asia. Our study included only those physicians and doctors who died after contracting COVID-19 from their respective workplaces. All available data about the country of origin, type of, sex, age, medical or surgical specialty, and date of death were included.

RESULTS

The total number of physician deaths reported due to COVID-19 in our study was 170, with half (87/170, 51%) of the deaths reported from Iran. Male physician deaths were reported to be 145 (145/170 = 85%). Internal Medicine (58.43%) was the most severely affected sub-specialty. The highest physician mortality rate in the general population recorded in Afghanistan (27/1000 deaths). General physicians from India [OR = 11.00(95% CI = 1.06-114.08), p = 0.045] and public sector medical practitioners from Pakistan [aOR = 4.52 (95% CI = 1.18-17.33), p = 0.028] were showing significant mortality when compared with other regions in multivariate logistic regression.

CONCLUSION

An increased number of physician deaths, owing to COVID-19, has been shown in South Asia. This could be due to decreased personal protective equipment and the poor health care management systems of the countries in the region to combat the pandemic. Future studies should provide detailed information of characteristics associated with physician mortalities along with the main complications arising due to the virus.

Phylogenetic and Drug-Resistance Analysis of HIV-1 Sequences From an Extensive Paediatric HIV-1 Outbreak in Larkana, Pakistan

Introduction

In April 2019, an HIV-1 outbreak among children occurred in Larkana, Pakistan, affecting more than a thousand children. It was assumed that the outbreak originated from a single source, namely a doctor at a private health facility. In this study, we performed subtype distribution, phylogenetic and drug-resistance analysis of HIV-1 sequences from 2019 outbreak in Larkana, Pakistan.

Methods

A total of 401 blood samples were collected between April–June 2019, from children infected with HIV-1 aged 0–15 years recruited into a case-control study to investigate the risk factors for HIV-1 transmission. Partial HIV-1 pol sequences were generated from 344 blood plasma samples to determine HIV-1 subtype and drug resistance mutations (DRM). Maximum-likelihood phylogenetics based on outbreak and reference sequences was used to identify transmission clusters and assess the relationship between outbreak and key population sequences between and within the determined clusters. Bayesian analysis was employed to identify the time to the most recent common recent ancestor (tMRCA) of the main Pakistani clusters.

Results

The HIV-1 circulating recombinant form (CRF) 02_AG and subtype A1 were most common among the outbreak sequences. Of the treatment-naïve participants, the two most common mutations were RT: E138A (8%) and RT: K219Q (8%). Four supported clusters within the outbreak were identified, and the median tMRCAs of the Larkana outbreak sequences were estimated to 2016 for both the CRF02_AG and the subtype A1 clusters. Furthermore, outbreak sequences exhibited no phylogenetic mixing with sequences from other high-risk groups of Pakistan.

Conclusion

The presence of multiple clusters indicated a multi-source outbreak, rather than a single source outbreak from a single health practitioner as previously suggested. The multiple introductions were likely a consequence of ongoing transmission within the high-risk groups of Larkana, and it is possible that the so-called Larkana strain was introduced into the general population through poor infection prevention control practices in healthcare settings. The study highlights the need to scale up HIV-1 prevention programmes among key population groups and improving infection prevention control in Pakistan.

Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan

BACKGROUND

We investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan.

MATERIALS AND METHODS

We studied ninety SARS-CoV-2 strains isolated between March and October 2020. Whole genome sequences from our laboratory and available genomes were used to investigate phylogeny, genetic variantion and mutation rates of SARS-CoV-2 strains in Pakistan. Site specific entropy analysis compared mutation rates between strains isolated before and after June 2020.

RESULTS

In March, strains belonging to L, S, V and GH clades were observed but by October, only L and GH strains were present. The highest diversity of clades was present in Sindh and Islamabad Capital Territory and the least in Punjab province. Initial introductions of SARS-CoV-2 GH (B.1.255, B.1) and S (A) clades were associated with overseas travelers. Additionally, GH (B.1.255, B.1, B.1.160, B.1.36), L (B, B.6, B.4), V (B.4) and S (A) clades were transmitted locally. SARS-CoV-2 genomes clustered with global strains except for ten which matched Pakistani isolates. RNA substitution rates were estimated at 5.86 x10-4. The most frequent mutations were 5' UTR 241C > T, Spike glycoprotein D614G, RNA dependent RNA polymerase (RdRp) P4715L and Orf3a Q57H. Strains up until June 2020 exhibited an overall higher mean and site-specific entropy as compared with sequences after June. Relative entropy was higher across GH as compared with GR and L clades. More sites were under selection pressure in GH strains but this was not significant for any particular site.

CONCLUSIONS

The higher entropy and diversity observed in early pandemic as compared with later strains suggests increasing stability of the genomes in subsequent COVID-19 waves. This would likely lead to the selection of site-specific changes that are advantageous to the virus, as has been currently observed through the pandemic.

Discrepancy between PCR based SARS-CoV-2 tests suggests the need to re-evaluate diagnostic assays

OBJECTIVE

We investigated the discrepancy between clinical and PCR-based diagnosis of COVID-19. We compared results of ten patients with mild to severe COVID-19. Respiratory samples from all cases were tested on the Roche SARS-CoV-2 (Cobas) assay, Filmarray RP2.1 (bioMereiux) and TaqPath™ COVID19 (Thermofisher) PCR assays.

RESULTS

Laboratory records of ten patients with mild to severe COVID-19 were examined. Initially, respiratory samples from the patients were tested as negative on the SARS-CoV-2 Roche^® assay. Further investigation using the BIOFIRE^® Filmarray RP2.1 assay identified SARS-CoV-2 as the pathogen in all ten cases. To investigate possible discrepancies between PCR assays, additional testing was conducted using the TaqPath™ COVID19 PCR. Eight of ten samples were positive for SARS-CoV-2 on the TaqPath assay. Further, Spike gene target failures (SGTF) were identified in three of these eight cases. Discrepancy between the three PCR assays could be due to variation in PCR efficiencies of the amplification reactions or, variation at primer binding sites. Strains with SGTF indicate the presence of new SARS-CoV-2 variant strains. Regular modification of gene targets in diagnostic assays may be necessary to maintain robustness and accuracy of SARS-CoV-2 diagnostic assays to avoid reduced case detection, under-surveillance, and missed opportunities for control.

Impact of duration of antibiotic prophylaxis on rates of surgical site infection (SSI) in patients undergoing mastectomy without immediate reconstruction, comparing a single prophylactic dose versus continued antibiotic prophylaxis postoperatively: a multicentre, double-blinded randomised control trial protocol

INTRODUCTION

In breast surgeries, prophylactic antibiotics given before the surgical incision as per Joint Commission Surgical Care Improvement Project guidelines have been shown to decrease the rate of postoperative infections. There is, however, no clear consensus on postoperative antibiotic prophylaxis in patients undergoing mastectomy with indwelling drains. This trial protocol proposes to study the difference in rates of surgical site infection (SSI) with or without continuation of postoperative antibiotics in patients undergoing mastectomy without immediate reconstruction and with indwelling drains.

METHODS AND ANALYSIS

In this multicentre, double-blinded clinical trial, all patients undergoing mastectomy (without immediate reconstruction) will receive a single prophylactic dose of preoperative antibiotics at induction of anaesthesia and will then get randomised to either continue antibiotic prophylaxis or a placebo postoperatively, for the duration of indwelling drains. The primary and secondary outcomes will be development of an SSI and antibiotic-associated adverse effects, respectively. Data will be collected through a standard questionnaire by wound assessors. Intention-to-treat analysis will be carried out using STATA V.12. For categorical variables, frequencies and percentages will be assessed by χ2 test/Fisher's exact test as appropriate. The quantitative variables will be computed by their mean±SD or median (IQR) and will be assessed by independent t-test/Mann-Whitney test as appropriate. Unadjusted and adjusted relative risk with their 95% CI will be reported using Cox proportional regression. A p value of <0.05 will be considered statistically significant.

ETHICS AND DISSEMINATION

Ethical approval has been obtained from each site's Ethical Review Board. The study background and procedure will be explained to the study participants and informed consent will be obtained. Participation in the study is voluntary. All data will be deidentified and kept confidential. The study findings will be published in scientific media and authorship guidelines of International Committee of Medical Journal Editors will be followed.

TRIAL REGISTRATION NUMBER

NCT04577846. (patient recruitment).

Comparison of risk factors and outcomes of Candida auris candidemia with non-Candida auris candidemia: A retrospective study from Pakistan

Candida auris has emerged as a nosocomial multi-drug resistant pathogen. This study aimed to compare the risk factors and outcomes of C. auris candidemia patients with non-C. auris candidemia, at a single center in Pakistan. A retrospective study compared 38 C. auris with 101 non-C. auris (36 C. albicans, 38 C. tropicalis, and 27 C. parapsilosis) candidemia patients between September 2014 and March 2017 at the Aga Khan University Hospital, Pakistan. Demographics, clinical history, management and outcomes were studied. Prior history of surgery (adjusted odds ratio [aOR] 4.9, 95% confidence interval [CI]: 1.4-17.5), antifungals exposure (aOR 38.3, 95% CI: 4.1-356) and prior MDR bacteria isolation (aOR 5.09, 95% CI: 1.6-15.9) were associated with C. auris candidemia. On survival analysis both groups of patients had similar outcome in terms of mortality (62.6% vs. 52.54%, hazard ratio [HR] 1.45, 95% CI: 0.84-2.4, P-value = .17) and microbiological failure rates (42.3% vs. 32.2%, HR 0.65, 95% CI: 0.35-1.2, P-value = .17) however, C. auris patients had a higher mean hospital stay (36.32 days vs. 14.8 days, P-value = <.001) and higher >15-day in-hospital stay from positive culture (HR 2.68, 95% CI: 1.1-6.3, P-value = .025). Antifungal susceptibility was different, with C. auris more often resistant to voriconazole (29.6% vs. 0%) and amphotericin (3.7 vs. 0%); though no echinocandin resistance was detected in either group. As opposed to other Candida species, C. auris candidemia occurred after nosocomial exposure, and its source was most commonly an indwelling line. Although these patients had a higher in-hospital stay, but there was no excess mortality when compared to other Candida species.

Factors associated with HIV infection among children in Larkana District, Pakistan: a matched case-control study

BACKGROUND

In April, 2019, an HIV outbreak predominantly affecting children occurred in Larkana District, Sindh, Pakistan. By December, 2019, 881 (4·0%) of 21 962 children screened for HIV had tested positive. We aimed to assess factors associated with HIV infection in this outbreak.

METHODS

In this individually matched case-control study, we sampled 406 cases (individuals aged <16 years who had registered for paediatric HIV care at the HIV Treatment Centre at Shaikh Zayed Children's Hospital in Larkana City, Pakistan) and 406 controls (individuals without HIV matched by age, sex, and neighbourhood residence, recruited through doorknocking at houses adjacent to case participants). An interviewer-administered questionnaire was used to collect data on possible risk factors for HIV acquisition and a blood sample was collected from all participants for hepatitis B and hepatitis C serology. Mothers of all participants underwent HIV testing. Odds ratios were estimated using conditional logistic regression to assess factors associated with HIV infection.

FINDINGS

406 case-control pairs were recruited between July 3 and Dec 26, 2019. Five pairs were excluded (three pairs had an age mismatch and two pairs were duplicate cases) and 401 were analysed. The prevalence of hepatitis B surface antigen was 18·2% (95% CI 14·5-22·3) among cases and 5·2% (3·3-7·9) among controls, and the prevalence of hepatitis C antibodies was 6·5% (95% CI 4·3-9·4) among cases and 1·0% (0·3-2·5) among controls. 28 (7%) of 397 mothers of cases for whom we had data, and no mothers of 394 controls, were HIV positive. In the 6 months before recruitment, 226 (56%) of 401 cases and 32 (8%) of 401 controls reported having more than ten injections, and 291 (73%) cases and 78 (19%) controls had received an intravenous infusion. At least one blood transfusion was reported in 56 (14%) cases and three (1%) controls in the past 2 years. HIV infection was associated with a history of more injections and infusions (adjusted odds ratio 1·63; 95% CI 1·30-2·04, p<0·0001), blood transfusion (336·75; 23·69-4787·01, p<0·0001), surgery (399·75, 13·99-11 419·39, p=0·0005), the child's mother being HIV positive or having died (3·13, 1·20-8·20, p=0·020), and increased frequency of private clinic (p<0·0001) and government hospital visits (p<0·0001), adjusting for confounders.

INTERPRETATION

The predominant mode of HIV transmission in this outbreak was parenteral, probably due to unsafe injection practices and poor blood safety practices. General practitioners across Pakistan need training and systems support in reducing injection use, and in providing safe injections and transfusions only when necessary.

FUNDING

Department of Pediatrics and Child Health, the Aga Khan University, Karachi, Pakistan.

Clinical characteristics and outcomes of COVID-19: Experience at a major tertiary care center in Pakistan

INTRODUCTION

Limited data exist on clinical characteristics and outcomes of hospitalized COVID-19 patients in low-middle income countries. We aimed to describe the clinical spectrum and outcomes of hospitalized COVID-19 patients at a tertiary-care center in Karachi, Pakistan.

METHODOLOGY

We conducted an observational study of adult COVID-19 patients hospitalized between February-June 2020. Patients with a discharge diagnosis of COVID-19 and PCR positivity were included. We created logistic regression models to understand association of clinical characteristics with illness severity and in-hospital mortality.

RESULTS

The study population comprised 445 patients [67% males, median age 53 (IQR 40-64) years]. Majority of patients (N = 268; 60%) had ≥ 1 co-morbid [37.5% hypertension, 36.4% diabetes]. In-hospital mortality was 13%. Age ≥ 60 (aOR] =1.92; 95 %CI = 1.23-3.03), shortness of breath (aOR=4.43; 95% CI=2.73-7.22), CRP ≥150mg/L (aOR:1.77; 95% CI=1.09-2.85), LDH ≥ 500 I.U/L (aOR:1.98; 95% CI=1.25-3.16), Neutrophil-to-Lymphocyte ratio (NLR) ≥5 (aOR:2.80; 95%CI = 1.77-4.42) and increase in serum creatinine (aOR:1.32; 95%CI=1.07-1.61) were independently associated with disease severity. Septic shock (aOR: 13.27; 95% CI=3.78-46.65), age ≥ 60 (aOR: 3.26; 95% CI=1.07-9.89), Ferritin ≥ 1500ng/ml (aOR: 3.78; 95% CI=1.21-11.8), NLR ≥ 5 (aOR: 4.04; 95% CI=1.14-14.35) and acute kidney injury (aOR: 5.52; 95% CI=1.78-17.06) were independent predictors of in-hospital mortality.

CONCLUSIONS

We found multiple predictors to be independently associated with in-hospital mortality, except diabetes and gender. Compared to reports from other countries, the in-hospital mortality among COVID-19 patients was lower, despite a high burden of co-morbidities. Further research is required to explore reasons behind this dichotomy.

COVID-19 pandemic: from origins to outcomes. A comprehensive review of viral pathogenesis, clinical manifestations, diagnostic evaluation, and management

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), the causative pathogen for the COVID-19, first emerged in Wuhan, China, in December 2019 and by March 2020, it was declared a pandemic. COVID-19 pandemic has overburdened healthcare systems in most countries and has led to massive economic losses. SARS-CoV-2 transmission typically occurs by respiratory droplets. The average incubation period is 6.4 days and presenting symptoms typically include fever, cough, dyspnea, myalgia or fatigue. While the majority of patients tend to have a mild illness, a minority of patients develop severe hypoxia requiring hospitalization and mechanical ventilation. Management is mostly supportive. However, several direct anti-viral agents, and immunomodulatory therapy with steroids and various cytokine blockers seem promising in early results. However, an effective vaccine has been established, which will help curb the pandemic.

Thrombosis with Thrombocytopenia Syndrome After Administration of AZD1222 or Ad26.COV2.S Vaccine for COVID-19: A Systematic Review

BACKGROUND

Cases of thrombosis with thrombocytopenia syndrome (TTS) have been reported following vaccination with AZD1222 or Ad26.COV2.S. This review aimed to explore the pathophysiology, epidemiology, diagnosis, management, and prognosis of TTS.

METHODS

A systematic review was conducted to identify evidence on TTS till 4th September 2021. Case reports and series reporting patient-level data were included. Descriptive statistics were reported and compared across patients with different sexes, age groups, vaccines, types of thrombosis, and outcomes.

FINDINGS

Sixty-two studies reporting 160 cases were included from 16 countries. Patients were predominantly females with a median age of 42.50 (22) years. AZD1222 was administered to 140 patients (87·5%). TTS onset occurred in a median of 9 (4) days after vaccination. Venous thrombosis was most common (61.0%). Most patients developed cerebral venous sinus thrombosis (CVST; 66.3%). CVST was significantly more common in female vs male patients (p = 0·001) and in patients aged <45 years vs ≥45 years (p = 0·004). The mortality rate was 36.2%, and patients with suspected TTS, venous thrombosis, CVST, pulmonary embolism, or intraneural complications, patients not managed with non-heparin anticoagulants or IVIG, patients receiving platelet transfusions, and patients requiring intensive care unit admission, mechanical ventilation, or inpatient neurosurgery were more likely to expire than recover.

INTERPRETATION

These findings help to understand the pathophysiology of TTS while also recommending diagnostic and management approaches to improve prognosis in patients.

FUNDING

This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.

1417. Clinical Features and Outcomes of raoultella terrigena Infections. A Single-Center Experience from Karachi, Pakistan

Background

Raoultella terrigena (formerly Klebsiella terrigena) is an environmental gram-negative rod, occasionally causing infections in humans, especially in elderly, immunosuppressed patients. Moreover, this organism tends to be multi-drug resistant, limiting treatment options. Evidence on clinical presentation and outcomes of this infection is limited; we conducted a cross-sectional study to get a better insight into these infections.

Methods

We conducted a cross-sectional study on all adult patients with clinical specimen positive for Raoultella terrigena at a 700-bedded tertiary care hospital in Karachi, Pakistan, between January 2013 to December 2018.

Results

A total of 58 patients with R. terrigena were identified. The median age was 61.5 years, and the male to female ratio was (60.9% vs. 39.1%). The most common site of infection was respiratory tract 28.3%, followed by urinary tract infections 26%, and central line-associated infections 15.2%. In 12 patients 22.6%, R. terrigena was a colonizer. Amongst infected cases, 23.6% were in shock, and of which 18.1% required vasopressors. 29.2% had respiratory failure requiring non-invasive ventilation in 13.9%, and mechanical ventilation in 15.3%. The previous history of multidrug-resistant organisms was present in 67.4% cases and the history of prior antibiotics use within the last six months was present in 78.3%. 91.3% of isolates were resistant to piperacillin-tazobactam and meropenem, 65.2% were resistant to colistimethate. However, tigecycline susceptibility maintained in 30.4% checked in n=31, 67.4% and fosfomycin sensitivity in 15.2% cases, checked in n=29, 63% cases. Eight patients lost to follow up. Majority of patients were treated with combination therapy n=31, 81.6% and meropenem plus colistemethate was the most commonly used combination n=11, 44%. The overall mortality rate was 44.7%. Among all recorded co-morbid conditions, chronic kidney disease was strongly associated with mortality (p= .029), as also the use of vasopressors (p= .005).Persons who had high (greater or equal to three) Charlson comorbidity index had high mortality (p=0.002).

Conclusion

R.terrigena is a highly drug-resistant organism with high mortality rate, and causes hospital-acquired respiratory tract infections in majority of patients.

Disclosures

All Authors: No reported disclosures

Subretinal abscess as an initial presentation of systemic nocardiosis

We report a case of subretinal abscess as the initial presentation of systemic nocardiosis. The patient was a known case of chronic inflammatory demyelinating polyneuropathy and on long-term immunosuppressants. He presented with a rapidly progressive, unilateral decline in visual acuity in the right eye. Dilated fundus examination showed a large whitish subretinal lesion. A working diagnosis of subretinal abscess was made. The appearance was highly suspicious for Nocardia abscess. On further direct questioning, it was noted that the patient had been experiencing low-grade fever and non-productive cough for 1 month. The patient was referred to infectious diseases for systemic work-up and a vitreous tap was done, along with intravitreal antibiotics. Blood culture and bronchoalveolar lavage both reported Nocardia species. Sensitivity-guided antibiotic therapy resulted in improved systemic condition and a quiet and comfortable right eye, but vision could not be saved due to late presentation.

Invasive pulmonary infection by Syncephalastrum species: Two case reports and review of literature

Background

Syncephalastrum species belong to the class Zygomycetes and order Mucorale. These are found in the environment and tropical soil, usually presenting as colonizers and rarely cause human infection. Syncephalastrum racemosum is a species of the genus Syncephalastrum and is the most commonly identified pathogen. Most cases are reported in immunocompromised individuals, such as patients on long term steroids, poorly controlled diabetes, or patients with malignancy.

Case presentation

We are describing two cases of rare fungal infection by Syncephalastrum species causing invasive pulmonary manifestation. Both patients had compromised immune status and presented with worsening dyspnea to the emergency room. Both had signs and symptoms of bilateral worsening pneumonia evident by chest X-ray showing bilateral pulmonary infiltrates. Syncephalastrum species were isolated from sputum cultures. Deoxycholate amphotericin B was started and the response was monitored. One patient expired while the other improved. Syncephalastrum species belong to class Mucormycosis, rarely causing invasive infection but when they do outcome is potentially fatal. Very few cases are reported worldwide so the clinical course is still unclear. To the best of our knowledge, these are the first two cases to be reported from Pakistan.

Conclusions

These two cases describe pneumonia as a result of concomitant infection by rare fungal speciesSyncephalastrum and MRSA in immunocompromised patients. Few cases are reported so limited data is available to understand complete disease implications. Mucormycosis is a therapeutic challenge because of the phylogenetic diversity, un-availability of any serological testing and invasive disease pattern.

COVID-19-associated pulmonary aspergillosis (CAPA) in patients admitted with severe COVID-19 pneumonia: An observational study from Pakistan

Background

Invasive aspergillosis is a well‐known complication of severe influenza pneumonia with acute respiratory distress syndrome (ARDS). However, recent studies are reporting emergence of aspergillosis in severe COVID‐19 pneumonia, named as COVID‐19‐associated pulmonary aspergillosis (CAPA).

Methods

A retrospective observational study was conducted in patients with severe COVID‐19 pneumonia from February 2020 to April 2020. Patients ≥18 years of age with clinical features and abnormal chest imaging with confirmed COVID‐19 by RT‐PCR for SARS‐CoV‐2 were included. CAPA was diagnosed based on clinical parameters, radiological findings and mycological data. Data were recorded on a structured proforma, and descriptive analysis was performed using Stata ver 12.1.

Results

A total of 147 patients with confirmed COVID‐19 and 23 (15.6%) patients requiring ICU admission were identified. Aspergillus species were isolated from tracheal aspirates of nine (39.1%) patients, and of these, five patients (21.7%) were diagnosed with CAPA and four (17.4%) had Aspergillus colonisation. The mean age of patients with CAPA was 69 years (Median age: 71, IQR: 24, Range: 51‐85), and 3/5 patients were male. The most frequent co‐morbid was diabetes mellitus (4/5). The overall fatality rate of COVID‐19 patients with aspergillosis was 44% (4/9). The cause of death was ARDS in all three patients with CAPA, and the median length of stay was 16 days (IQR: 10; Range 6‐35 days).

Conclusion

This study highlights the need for comparative studies to establish whether there is an association of aspergillosis and COVID‐19 and the need for screening for fungal infections in severe COVID‐19 patients with certain risk factors.

Investigation of an extensive outbreak of HIV infection among children in Sindh, Pakistan: protocol for a matched casecontrol study

INTRODUCTION

In April 2019, 14 children were diagnosed with HIV infection by a private healthcare provider in Larkana district, Sindh province, Pakistan. Over the next 3 months, 930 individuals were diagnosed with HIV, >80% below 16 years, the largest ever outbreak of HIV in children in Pakistan. In this protocol paper, we describe research methods for assessing likely modes of HIV transmission in this outbreak and investigate spatial and molecular epidemiology.

METHODS AND ANALYSIS

A matched case-control study will be conducted with 406 cases recruited. Cases will be children aged below 16 years registered for care at the HIV treatment centre at Shaikh Zayed Children Hospital in Larkana City. Controls will be children who are HIV-uninfected (confirmed by a rapid HIV test) matched 1:1 by age (within 1 year), sex and neighbourhood. Following written informed consent from the guardian, a structured questionnaire will be administered to collect data on sociodemographic indices and exposure to risk factors for parenteral, vertical and sexual (only among those aged above 10 years) HIV transmission. A blood sample will be collected for hepatitis B and C serology (cases and controls) and HIV lineage studies (cases only). Mothers of participants will be tested for HIV to investigate the possibility of mother-to-child transmission. Conditional logistic regression will be used to investigate the association of a priori defined risk factors with HIV infection. Phylogenetic analyses will be conducted. Global positioning system coordinates of participants' addresses will be collected to investigate concordance between the genetic and spatial epidemiology.

ETHICS AND DISSEMINATION

Ethical approval was granted by the Ethics Review Committee of the Aga Khan University, Karachi. Study results will be shared with Sindh and National AIDS Control Programs, relevant governmental and non-governmental organisations, presented at national and international research conferences and published in international peer-reviewed scientific journals.

Risk factors for mortality of patients with ceftriaxone resistant E. coli bacteremia receiving carbapenem versus beta lactam/beta lactamase inhibitor therapy

OBJECTIVE

Extended spectrum β-lactamases (ESBL) producing Enterobacteriaceae predominantly E. coli and K. pneumoniae bacteremia have limited treatment options and high mortality. The objective was to determine the risk factors for in-hospital mortality particularly treatment with carbapenem versus beta lactam/beta lactamase combination (BL/BLI) in patients with ceftriaxone resistant E. coli bacteremia. A retrospective cohort study was conducted at the Aga Khan University, Karachi, Pakistan. Adult patients with sepsis and monomicrobial ceftriaxone resistant E. coli bacteremia were enrolled. Factors associated with mortality in patients were determined using logistic regression analysis.

RESULTS

Mortality rate was 37% in those empirically treated with carbapenem compared to 20% treated with BL/BLI combination therapy (p-value: 0.012) and was 21% in those treated with a carbapenem compared to 13% in patients definitively treated with BL/BLI combination therapy (p-value: 0.152). In multivariable logistic regression analysis, only Pitt bacteremia score of ≥ four was significantly associated with mortality (OR: 7.7 CI 2.6-22.8) while a urinary source of bacteremia was protective (OR: 0.26 CI 0.11-0.58). In-hospital mortality in patients with Ceftriaxone resistant E. coli bacteremia did not differ in patients treated with either a carbapenem or BL/BLI combination. However, Pitt bacteremia score of ≥ 4 was strongly associated with mortality.

2416. Risk Factors and Outcomes of Bacteremia Caused by Carbapenem-Resistant Enterobacteriaceae Compared With Carbapenem Susceptible Enterobacteriaceae

Background

Due to shrinking therapeutic options, infections due to Carbapenem-resistant enterobacteriaceae (CRE) are an urgent threat in healthcare systems across the world. While the CRE phenotype is determined by a number a different genes, the metallo β-lactamases such as the NDM, are particularly prevalent in the South Asian region. Data regarding infections with CRE caused by these strains is relatively limited. Our objective was to compare the risk factors and outcomes (mortality and length of hospitalization) of bacteremia secondary to CRE with bacteremia secondary to carbapenem susceptible enterobacteriaceae (CSE).

Methods

We conducted a cross-sectional study on patients admitted between 2013 and 2016, to a large tertiary care hospital in Karachi, Pakistan. Patients with CRE bacteremia were matched for the same year with patients with bacteremia due to CSE. Patients with polymicrobial blood cultures were excluded. Clinical data of these patients were obtained using a structured performa.

Results

A total of 131 patients were enrolled (65 CRE and 66 CSE). The mean age was similar in both groups (51.8 years and 57.1 years in CRE and CSE patients respectively). Compared with CSE, CRE bacteremia was more likely to occur in patients with Diabetes Mellitus or those with a tracheostomy (P = 0.002 and 0.014, respectively). The most common source of CRE bacteremia was central line associated (24.6% of all cases) as opposed to urinary tract infections in those with CSE bacteremia (62.1% of all cases). Fewer patients with CRE bacteremia received appropriate antibiotics (72.3% vs. 81.8%). Mortality was over three times higher in patients with CRE (41.5% vs. 12.1%, P = 0.001). The mortality remained higher when adjusted for the severity of illness using the PITT-bacteremia score. Increased mortality was also associated with central venous catheterization in both CRE and CSE bacteremia, while urinary catheterization and hemodialysis were associated with mortality in patients in CSE bacteremia only. While length of ICU stay was similar between the two groups, the median length of hospital stay was longer in patients with CRE (median of 8 days vs. 6 days, P = 0.021)

Conclusion

CRE bacteremia was more likely associated with central lines and led to significantly higher mortality and length of stay.

Disclosures

All authors: No reported disclosures.

Relationship Between Staphylococcus aureus Carriage and Surgical Site Infections Following Total Hip and Knee Arthroplasty in the South Asian Population: Protocol for a Prospective Cohort Study

Background

Surgical site infections following total hip or knee arthroplasties have a reported rate of 0.49%-2.5% and can cause significant morbidity as well as tripling the cost of health care expenses. Both methicillin sensitive and methicillin resistant strains of Staphylococcus aureus surgical site infections have been established as a major risk factor for postoperative surgical site infections. S. aureus colonizes the nose, axillae, and perineal region in up to 20%-30% of individuals. Although the literature has reported a higher prevalence of methicillin resistant S. aureus in the South Asian population, routine preoperative screening and prophylaxis have not yet been implemented.

Objective

The primary objective of our study is to identify the relationship between preoperative colonization status of S. aureus and incidence of postoperative surgical site infections in patients undergoing following total hip and knee arthroplasties. As part of the secondary objectives of this study, we will also investigate patient characteristics acting as risk factors for S. aureus colonization as well as the outcomes of total hip and knee arthroplasty patients which are affected by surgical site infections.

Methods

This prospective cohort study will comprise of screening all patients older than 18 years of age admitted to the Aga Khan University Hospital for a primary total hip or knee arthroplasty for preoperative colonization with S. aureus. The patients will be followed postoperatively for up to one year following the surgery to assess the incidence of surgical site infections. The study duration will be 2 years (March 2018 to March 2020). For the purpose of screening, pooled swabs will be taken from the nose, axillae, and groin of each patient and inoculated in a brain heart infusion, followed by subculture onto mannitol salt agar and sheep blood agar. For methicillin resistant S. aureus identification, a cefoxitin disk screen will be done. Data will be analyzed using SPSS v23 and both univariate and multivariate regression analysis will be conducted.

Results

Data collection for this study will commence at the Aga Khan University Hospital, Pakistan during March 2018.

Conclusions

This study will not only estimate the true burden caused by S. aureus in the population under study but will also help identify the patients at a high risk of surgical site infections so that appropriate interventions, including prophylaxis with antibiotics such as muciprocin ointment or linezolid, can be made. Given the differences in lifestyle, quality, and affordability of health care and the geographical variation in patterns of antibiotic resistance, this study will contribute significantly to providing incentive for routine screening and prophylaxis for S. aureus including methicillin resistant S. aureus colonization in the South Asian population.

Registered Report Identifier

RR1-10.2196/10219

Hypermucoviscous Klebsiella syndrome it's in the community!

Hypermucoviscous Klebsiella syndrome is a unique syndrome caused by a new variant of Klebsiella pneumoniae (KP), characterized by abscess formation at distant body sites. This emerging KP strain is different from the usual classic strains in having the rmp gene which increases capsule formation making this strain resistant to phagocytosis and helping in its dissemination to distant organs. A 50 years old diabetic man presented with facial swelling after dental procedure which progressively increased despite being on antibiotics. On examination he was febrile, had neck swelling with signs of inflammation and tender hepatomegaly. Ultrasonography showed submental and liver abscesses which were subsequently drained and both cultures isolated KP with hypermucoid colonies on agar plate and a positive string test indicating the presence of this new hypervirulent strain of KP. Therefore, a diagnosis of Hypermucoviscous Klebsiella syndrome should be considered in all patients who present with KP infection with multiple organ abscesses..

Mortality In Patients With Respiratory And Nonrespiratory Carbapenem Resistant-Multidrug Resistant Acinetobacter Infections

BACKGROUND

Mortality from carbapenem-multi-drug resistant Acinetobacter infections may vary according to site of infection. The objective of this study was to compare mortality in respiratory vs. non-respiratory infection with Carbapenem-Multi-drug Resistant Acinetobacter (C-MRAB).

METHODS

We conducted a prospective cohort study to compare mortality rate in patients with respiratory vs. nonrespiratory infection (n=30 each).

RESULTS

Results showed that mortality was 40% in the respiratory group compared to 23% in non-respiratory group; the difference was not statistically significant (p=0.165, RR=1.71, CI=0.73-3.75). There was a significantly higher prior admission rate in patients with respiratory infection (p=0.028). Logistic regression did not reveal any modifier effect from other variables.

CONCLUSIONS

This study showed no significant difference in mortality in patients with carbapenem-multi-drug resistant acinetobacter respiratory vs. non-respiratory infections.

Comparison of the clinical presentations of Naegleria fowleri primary amoebic meningoencephalitis with pneumococcal meningitis: a case-control study

BACKGROUND

Primary amoebic meningoencephalitis (PAM) is a rare but fatal infection caused by Naegleria fowleri. The infection is acquired by deep nasal irrigation with infected water. Patients present with signs and symptoms similar to pneumococcal meningitis, leading to delayed diagnosis and treatment and hence high mortality.

METHODS

We conducted a case-control study comparing culture proven cases of PAM with pneumococcal meningitis presenting to our center between April 2008 and September 2014. Only patients with blood and/or cerebrospinal fluid cultures positive for Streptococcus pneumoniae during the same time period were included for comparison.

RESULTS

There were 19 cases of PAM and pneumococcal meningitis, each. When comparing PAM with pneumococcal meningitis, patients with PAM were more likely to be male (89.5 vs. 36.8 %), younger (mean age: 30 vs. 59 years), present with seizures (42.1 vs. 5.3 %). Both groups of patients presented with similar vital signs and there were no remarkable differences on physical examinations, Glasgow Coma Scale scores, laboratory and radiological investigations and cerebrospinal fluid parameters. PAM was also more likely to present if the city's average maximum temperature was higher in the previous week (mean: 34.6 vs. 30 °C). There was history of fresh water contact in only one patient. On multivariate analysis, PAM was more likely if patients presented when the city's average maximum temperature was high, being young males.

CONCLUSION

PAM and pneumococcal meningitis remain virtually indistinguishable; however, these predictive features should be validated in a prospective study and may lead to a viable algorithm for early management of these patients.

International Nosocomial Infection Control Consortium (INICC) report, data summary of 43 countries for 2007-2012. Device-associated module

We report the results of an International Nosocomial Infection Control Consortium (INICC) surveillance study from January 2007-December 2012 in 503 intensive care units (ICUs) in Latin America, Asia, Africa, and Europe. During the 6-year study using the Centers for Disease Control and Prevention's (CDC) U.S. National Healthcare Safety Network (NHSN) definitions for device-associated health care-associated infection (DA-HAI), we collected prospective data from 605,310 patients hospitalized in the INICC's ICUs for an aggregate of 3,338,396 days. Although device utilization in the INICC's ICUs was similar to that reported from ICUs in the U.S. in the CDC's NHSN, rates of device-associated nosocomial infection were higher in the ICUs of the INICC hospitals: the pooled rate of central line-associated bloodstream infection in the INICC's ICUs, 4.9 per 1,000 central line days, is nearly 5-fold higher than the 0.9 per 1,000 central line days reported from comparable U.S. ICUs. The overall rate of ventilator-associated pneumonia was also higher (16.8 vs 1.1 per 1,000 ventilator days) as was the rate of catheter-associated urinary tract infection (5.5 vs 1.3 per 1,000 catheter days). Frequencies of resistance of Pseudomonas isolates to amikacin (42.8% vs 10%) and imipenem (42.4% vs 26.1%) and Klebsiella pneumoniae isolates to ceftazidime (71.2% vs 28.8%) and imipenem (19.6% vs 12.8%) were also higher in the INICC's ICUs compared with the ICUs of the CDC's NHSN.

A novel method of surgical site infection surveillance after cardiac surgery by active participation of stake holders

We describe a comprehensive surveillance system involving infection control practitioners, surgeons, administrative staff, and patients aimed at improving the postdischarge surveillance of surgical site infections. The system was able to detect 22 infections out of 538 procedures, 95% of which were detected during the postdischarge period.

Pulmonary nocardiosis: a comparative analysis of Nocardia asteroides and non-asteroides species

Our study compares the risk factors, clinical presentations and outcomes of pulmonary infections caused by Nocardia asteroides and non-asteroides species. We performed a retrospective cohort study comparing pulmonary infections by both species in patients presenting to a tertiary care hospital in Karachi, Pakistan. Forty-one patients were identified with pulmonary nocardiosis, with 58.5% belonging to the N. asteroids complex. The most common clinical findings were fever and a cough for both groups, with lobar infiltrates being the most common finding on chest radiographs. In vitro testing showed a sensitivity of all species to trimethoprim-sulfamethoxazole (TMP-SMZ), aminoglycosides, ceftriaxone and imipenem. The majority of the patients were treated with TMP-SMZ in combination with other drugs. The results of our study suggest that there is no significant difference in the risk factors, presentations and outcomes of pulmonary infections by N. asteroides and non-asteroides species. Immunocompromised patients are more likely to have unfavorable outcomes.

Primary amebic meningoencephalitis caused by Naegleria fowleri, Karachi, Pakistan

We report 13 cases of Naegleria fowleri primary amebic meningoencephalitis in persons in Karachi, Pakistan, who had no history of aquatic activities. Infection likely occurred through ablution with tap water. An increase in primary amebic meningoencephalitis cases may be attributed to rising temperatures, reduced levels of chlorine in potable water, or deteriorating water distribution systems.

Rhinocladiella mackenziei as an emerging cause of cerebral phaeohyphomycosis in Pakistan: a case series

Six cases of Rhinocladiella mackenziei cerebral phaeohyphomycosis are being reported for the first time in Pakistan. Identification was confirmed by DNA sequencing (isolates and fixed tissue). Diabetes, head trauma, immunosuppressive treatment, and postpartum state were present in 4 cases. Two survivals and 3 fatalities occurred, with 1 patient lost to follow-up.