Coordination strategies and concept of operations implemented during activation of public health emergency operations center for COVID-19 response in Pakistan

Public health emergency management systems encountered difficulties in developing countries, especially in Pakistan. The COVID-19 pandemic was extremely challenging for different agencies/departments in Pakistan. Health emergency management depends on a well-established public health emergency operations center that could generate a coordinated response to emergencies. We conducted an assessment of public health emergency response coordination implemented during the COVID-19 at strategic level. This was mix-method qualitative study. Primary data was collected by using a structured questionnaire, and secondary data was collected by desk review. The agencies engaged in pandemic response at the national level in Pakistan were included in the assessment. The overall score of the emergency response coordination system during COVID-19 was 49% for all agencies. We found that agencies faced challenges in leadership, legislation, and financing issues during the pandemic response (44%). None of the agencies had a fully developed framework for joint planning and response system for health emergencies. Roles and responsibilities attached to designated agencies in response were relatively clear (55%) for most of the agencies. Effective public health emergency response is based on multi-departmental coordination, resource mobilization, and clear roles for each agency. Pakistan must proactively address these challenges for pandemic response in future.

Ten golden rules for optimal antibiotic use in hospital settings: the WARNING call to action

Antibiotics are recognized widely for their benefits when used appropriately. However, they are often used inappropriately despite the importance of responsible use within good clinical practice. Effective antibiotic treatment is an essential component of universal healthcare, and it is a global responsibility to ensure appropriate use. Currently, pharmaceutical companies have little incentive to develop new antibiotics due to scientific, regulatory, and financial barriers, further emphasizing the importance of appropriate antibiotic use. To address this issue, the Global Alliance for Infections in Surgery established an international multidisciplinary task force of 295 experts from 115 countries with different backgrounds. The task force developed a position statement called WARNING (Worldwide Antimicrobial Resistance National/International Network Group) aimed at raising awareness of antimicrobial resistance and improving antibiotic prescribing practices worldwide. The statement outlined is 10 axioms, or "golden rules," for the appropriate use of antibiotics that all healthcare workers should consistently adhere in clinical practice.

Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes

Background

The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000).

Methods

This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch.

Results

Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes.

Conclusions

The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies.

Funding

No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]).

Antibiotic Susceptibility Surveillance in the Punjab Province of Pakistan: Findings and Implications

Background and Objectives: The increase in antimicrobial resistance (AMR) across countries has seriously impacted the effective management of infectious diseases, with subsequent impact on morbidity, mortality and costs. This includes Pakistan. Antimicrobial surveillance activities should be mandatory to continually assess the extent of multidrug-resistant bacteria and the implications for future empiric prescribing. The objective of this retrospective observational study was to monitor the susceptibility pattern of microbes in Pakistan. Materials and Methods: Clinical samples from seven laboratories in Punjab, Pakistan were collected between January 2018 and April 2019, with Punjab being the most populous province in Pakistan. The isolates were identified and their antimicrobial susceptibility was tested using the Kirby-Bauer disc diffusion assay and micro broth dilution methods. The antibiotics assessed were those typically prescribed in Pakistan. Results: In total, 2523 bacterial cultural reports were studied. The most frequently isolated pathogens were Staphylococcus aureus (866, 34.3%), followed by Escherichia coli (814, 32.2%), Pseudomonas aeruginosa (454, 18.0%) and Klebsiella pneumoniae (269, 10.7%). Most pathogens were isolated from pus (1464, 58.0%), followed by urine (718, 28.5%), blood (164, 6.5%) and sputum (81, 3.2%). Conclusions: The findings suggest that current antimicrobial options are severally restricted in Pakistan due to the emergence of multidrug-resistant pathogens. This calls for urgent actions including initiating antimicrobial stewardship programs to enhance prudent prescribing of antibiotics. This includes agreeing on appropriate empiric therapy as part of agreed guidelines, in line with the WHO EML and AWaRe book, whilst awaiting culture reports. This is alongside other measures to reduce inappropriate antimicrobial prescribing and reverse the threat of rising AMR.

Point Prevalence Survey of Antimicrobial Use in Selected Tertiary Care Hospitals of Pakistan Using WHO Methodology: Results and Inferences

Background and objectives: The inappropriate use of antibiotics in hospitals can potentially lead to the development and spread of antibiotic resistance, increased mortality, and high economic burden. The objective of the study was to assess current patterns of antibiotic use in leading hospitals of Pakistan. Moreover, the information collected can support in policy-making and hospital interventions aiming to improve antibiotic prescription and use. Methodology and materials: A point prevalence survey was carried out with data abstracted principally from patient medical records from 14 tertiary care hospitals. Data were collected through the standardized online tool KOBO application for smart phones and laptops. For data analysis, SPSS Software was used. The association of risk factors with antimicrobial use was calculated using inferential statistics. Results: Among the surveyed patients, the prevalence of antibiotic use was 75% on average in the selected hospitals. The most common classes of antibiotics prescribed were third-generation cephalosporin (38.5%). Furthermore, 59% of the patients were prescribed one while 32% of the patients were prescribed two antibiotics. Whereas the most common indication for antibiotic use was surgical prophylaxis (33%). There is no antimicrobial guideline or policy for 61.9% of antimicrobials in the respected hospitals. Conclusions: It was observed in the survey that there is an urgent need to review the excessive use of empiric antimicrobials and surgical prophylaxis. Programs should be initiated to address this issue, which includes developing antibiotic guidelines and formularies especially for empiric use as well as implementing antimicrobial stewardship activities.

Antibiotic Utilization Patterns for Different Wound Types among Surgical Patients: Findings and Implications

Antimicrobial prophylaxis is effective in reducing the rate of surgical site infections (SSIs) post-operatively. However, there are concerns with the extent of prophylaxis post-operatively, especially in low- and middle-income countries (LMICs). This increases antimicrobial resistance (AMR), which is a key issue in Pakistan. Consequently, we conducted an observational cross-sectional study on 583 patients undergoing surgery at a leading teaching hospital in Pakistan with respect to the choice, time and duration of antimicrobials to prevent SSIs. The identified variables included post-operative prophylactic antimicrobials given to all patients for all surgical procedures. In addition, cephalosporins were frequently used for all surgical procedures, and among these, the use of third-generation cephalosporins was common. The duration of post-operative prophylaxis was 3-4 days, appreciably longer than the suggestions of the guidelines, with most patients prescribed antimicrobials until discharge. The inappropriate choice of antimicrobials combined with prolonged post-operative antibiotic administration need to be addressed. This includes appropriate interventions, such as antimicrobial stewardship programs, which have been successful in other LMICs to improve antibiotic utilization associated with SSIs and to reduce AMR.

In Silico Analysis of SARS-CoV-2 Spike Proteins of Different Field Variants

Coronaviruses belong to the group of RNA family of viruses that trigger diseases in birds, humans, and mammals, which can cause respiratory tract infections. The COVID-19 pandemic has badly affected every part of the world. Our study aimed to explore the genome of SARS-CoV-2, followed by in silico analysis of its proteins. Different nucleotide and protein variants of SARS-CoV-2 were retrieved from NCBI. Contigs and consensus sequences were developed to identify these variants using SnapGene. Data of the variants that significantly differed from each other was run through Predict Protein software to understand the changes produced in the protein structure. The SOPMA web server was used to predict the secondary structure of the proteins. Tertiary structure details of the selected proteins were analyzed using the web server SWISS-MODEL. Sequencing results showed numerous single nucleotide polymorphisms in the surface glycoprotein, nucleocapsid, ORF1a, and ORF1ab polyprotein while the envelope, membrane, ORF3a, ORF6, ORF7a, ORF8, and ORF10 genes had no or few SNPs. Contigs were used to identify variations in the Alpha and Delta variants of SARS-CoV-2 with the reference strain (Wuhan). Some of the secondary structures of the SARS-CoV-2 proteins were predicted by using Sopma software and were further compared with reference strains of SARS-CoV-2 (Wuhan) proteins. The tertiary structure details of only spike proteins were analyzed through the SWISS-MODEL and Ramachandran plots. Through the Swiss-model, a comparison of the tertiary structure model of the SARS-CoV-2 spike protein of the Alpha and Delta variants was made with the reference strain (Wuhan). Alpha and Delta variants of the SARS-CoV-2 isolates submitted in GISAID from Pakistan with changes in structural and nonstructural proteins were compared with the reference strain, and 3D structure mapping of the spike glycoprotein and mutations in the amino acids were seen. The surprisingly increased rate of SARS-CoV-2 transmission has forced numerous countries to impose a total lockdown due to an unusual occurrence. In this research, we employed in silico computational tools to analyze the SARS-CoV-2 genomes worldwide to detect vital variations in structural proteins and dynamic changes in all SARS-CoV-2 proteins, mainly spike proteins, produced due to many mutations. Our analysis revealed substantial differences in the functionality, immunological, physicochemical, and structural variations in the SARS-CoV-2 isolates. However, the real impact of these SNPs can only be determined further by experiments. Our results can aid in vivo and in vitro experiments in the future.

Impact of Positive Culture Reports of E. coli or MSSA on De-Escalation of Antibiotic Use in a Teaching Hospital in Pakistan and the Implications

Background

Antibiotic de-escalation is a key element of antimicrobial stewardship programs that restrict the spread and emergence of resistance. This study was performed to evaluate the impact of positive culture sensitivity reports of E. coli or Methicillin sensitive Staphylococcus aureus (MSSA) on de-escalation of antibiotic therapy.

Methods

This prospective observational study was performed on 256 infected patients. The samples were obtained principally from the pus of infected sites for the identification of pathogens and culture-sensitivity testing. The data were collected from patient medical files, which included their demographic data, sample type, causative microbe and antimicrobial treatment as empiric or definitive treatment based on cultures. Data were analyzed using SPSS.

Results

Of 256 isolated microbes, 138 (53.9%) were MSSA and 118 were E. coli (46.1%). MSSA showed 100% sensitivity to cefoxitin, oxacillin, vancomycin, fosfomycin, colistin and more than 90% to linezolid (95.3%), tigecycline (93.1%), chloramphenicol (92.2%) and amikacin (90.2%). E. coli showed 100% sensitivity to only fosfomycin and more than 90% to colistin (96.7%), polymyxin-B (95.1%) and tigecycline (92.9%). The high use of cefoperazone+sulbactam (151), amikacin (149), ceftriaxone (33), metronidazole (30) and piperacillin + tazobactam (22) was seen with empiric prescribing. Following susceptibility testing, the most common antibiotics prescribed for E. coli were meropenem IV (34), amikacin (34), ciprofloxacin (29) and cefoperazone+sulbactam (25). For MSSA cases, linezolid (48), clindamycin (30), cefoperazone+ sulbactam IV (16) and amikacin (15) was used commonly. Overall, there was 23% reduction in antibiotic use in case of E. coli and 43% reduction in MSSA cases.

Conclusion

Culture sensitivity reports helped in the de-escalation of antimicrobial therapy, reducing the prescribing of especially broad-spectrum antibiotics. Consequently, it is recommended that local hospital guidelines be developed based on local antimicrobial susceptibility patterns while preventing the unnecessary use of broad-spectrum antibiotics for empiric treatment.

Distribution of mcr-1 Harboring Hypervirulent Klebsiella pneumoniae in Clinical Specimens and Lytic Activity of Bacteriophage KpnM Against Isolates

Background

The World Health Organization (WHO) has declared the multi-drug resistant (MDR) Klebsiella pneumoniae as one of the critical bacterial pathogens. The dearth of new antibiotics and inadequate therapeutic options necessitate finding alternative options. Bacteriophages are known as enemies of bacteria and are well-recognized to fight MDR pathogens.

Methods

A total of 150 samples were collected from different clinical specimens through a convenient sampling technique. Isolation, identification, and antibiotic susceptibility testing (AST) of K. pneumoniae were done by standard and validated microbiological procedures. Molecular identification of virulence factors and antibiotic resistance genes (ARGs) was carried out through polymerase chain reaction (PCR) by using specific primers. For bacteriophage isolation, hospital sewage samples were processed for phage enrichment, purification, and further characterization ie, transmission electron microscopy (TEM) and stability testing, etc. followed by evaluation of the lytic potential of the phage.

Results

Overall, a total of 41% of isolates of K. pneumoniae were observed as hypervirulent K. pneumoniae (hvKp). Among hvKp, a total of 12 (42%) were detected as MDR hvKp. A total of 37% of all MDR isolates were found resistant to colistin, and 66% of the colistin resistance isolates were recorded as mcr-1 positive. Isolated phage KpnM had shown lytic activity against 53 (79%) K. pneumoniae isolates. Remarkably, all 8 mcr-1 harboring MDR hvKp and non-hvKp isolates were susceptible to KpnM phage.

Conclusion

Significant distribution of mcr-1 harboring hypervirulent Klebsiella pneumoniae was observed in clinical specimens, which is worrisome for the health system of the country. Characterized phage KpnM exhibited encouraging results and showed the lytic activity against the mcr-1 harboring hvKp isolates, which may be used as a prospective alternative control strategy to fight this ominous bacterium.

Distribution and genetic diversity of multi-drug-resistant Klebsiella pneumoniae at the human–animal–environment interface in Pakistan

Klebsiella pneumoniae is ubiquitous and known to be a notorious pathogen of humans, animals, and plant-based foods. K. pneumoniae is a recognized trafficker of antibiotic resistance genes (ARGs) between and from different ecological niches. A total of 775 samples (n = 775) were collected from September 2017 to August 2019 from humans, animals, and environmental sources by applying the random convenient sampling technique. A total of 120 (15.7%) samples were confirmed as K. pneumoniae. The distribution of K. pneumoniae among humans, the environment, and animals was 17.1, 12.38, and 10%, respectively. Isolates have shown significant resistance against all the subjected antibiotics agents except colistin. ARGs profiling revealed that the highest percentage prevalence (67.5%) of bla_CTX–M was estimated in the isolates, and various carbapenem resistance genes that were found in the study were bla_NDM–1 (43.3%), bla_OXA–48 (38%), and (1.67%) bla_KPC–2. Overall, 21 distinct sequence types (ST) and 13 clonal complexes (CCs) were found through the multi-locus sequence typing (MLST) analysis. Taking together, the distribution of multi-drug resistance (MDR) K. pneumoniae clones in the  community and associated environment is alarming for the health care system of the country. Health policymakers should consider the role of all the integral parts of humans, animals, and the associated environment intently to cope with this serious public and animal health concern.

OUP accepted manuscript

STUDY QUESTION

What is the scope of literature regarding women’s reproductive span in terms of definitions, trends and determinants?

SUMMARY ANSWER

The scoping review found a wide variation in definitions, trends and determinants of biological, social and effective women’s reproductive span.

WHAT IS KNOWN ALREADY

A woman’s reproductive span refers to her childbearing years. Its span influences a woman’s reproductive decisions.

STUDY DESIGN, SIZE, DURATION

A systematic scoping review was conducted. We searched MEDLINE, PubMed, JSTOR, CINAHL, Web of Science and Scopus electronic databases from inception to January 2021 without imposing language or date restrictions. We searched unpublished sources including the Global Burden of Disease, Demographic and Health Surveys, and National Health and Nutrition Examination Surveys. The list of relevant references was searched by hand. Sixty-seven reports on women’s reproductive span were included in this review.

PARTICIPANTS/MATERIALS, SETTING, METHODS

This scoping systematic review followed an established framework. The reporting of this scoping review followed the reporting requirements provided in the Preferred Reporting Items for Systematic Reviews and Meta-Analyses, Extension for Scoping Reviews. Identified records were independently screened and data were extracted. We performed conceptual synthesis by grouping the studies by available concepts of reproductive span and then summarized definitions, measures used, temporal trends, determinants, and broad findings of implications on population demographics and assisted reproduction. Structured tabulation and graphical synthesis were used to show patterns in the data and convey detailed information efficiently, along with a narrative commentary.

MAIN RESULTS AND THE ROLE OF CHANCE

A total of 67 relevant reports on women’s reproductive span were published between 1980 and 2020 from 74 countries. Most reports (42/67) were cross-sectional in design. Literature on reproductive span was conceptually grouped as biological (the interval between age at menarche and age at menopause), effective (when a woman is both fertile and engaging in sexual activity) and social (period of exposure to sexual activity). We summarized the working definitions, trends and determinants of each concept. Few articles addressed implications on demographics and assisted reproduction.

LIMITATIONS, REASONS FOR CAUTION

A formal assessment of methodological quality of the included studies was not performed because the aim of this review was to provide an overview of the existing evidence base regardless of quality.

WIDER IMPLICATIONS OF THE FINDINGS

The review produced a comprehensive set of possible definitions of women’s reproductive span, trends, and potential determinants. Further advancement of these findings will involve collaboration with relevant stakeholders to rate the importance of each definition in relation to demography and fertility care, outline a set of core definitions, identify implications for policy, practice or research and define future research opportunities to explore linkages between reproductive spans, their determinants, and the need for assisted reproduction.

STUDY FUNDING/COMPETING INTEREST(S)

This work received funding from the UNDP-UNFPA-UNICEF-WHO-World Bank Special Programme of Research, Development and Research Training in Human Reproduction (HRP), a cosponsored programme executed by the World Health Organization (WHO). The authors had no competing interests.

STUDY REGISTRATION NUMBER

N/A.

Antibiotic consumption at community pharmacies: A multicenter repeated prevalence surveillance using WHO methodology

Background:

Antibiotics are losing their effectiveness because of the rapid emergence of resistant bacteria. Unnecessary antimicrobial use increases antimicrobial resistance (AMR). There are currently no published data on antibiotic consumption in Pakistan at the community level. This is a concern given high levels of self-purchasing of antibiotics in Pakistan and variable knowledge regarding antibiotics and AMR among physicians and pharmacists.

Objective:

The objective of this repeated prevalence survey was to assess the pattern of antibiotic consumption data among different community pharmacies to provide a baseline for developing future pertinent initiatives.

Methods:

A multicenter repeated prevalence survey conducted among community pharmacies in Lahore, a metropolitan city with a population of approximately 10 million people, from October to December 2017 using the World Health Organization (WHO) methodology for a global program on surveillance of antimicrobial consumption.

Results:

The total number of defined daily doses (DDDs) dispensed per patient ranged from 0.1 to 50.0. In most cases, two DDDs per patient were dispensed from pharmacies. Co-amoxiclav was the most commonly dispensed antibiotic with a total number of DDDs at 1018.15. Co-amoxiclav was followed by ciprofloxacin with a total number of 486.6 DDDs and azithromycin with a total number of 472.66 DDDs. The least consumed antibiotics were cefadroxil, cefotaxime, amikacin, and ofloxacin, with overall consumption highest in December.

Conclusion:

The study indicated high antibiotic usage among community pharmacies in Lahore, Pakistan particularly broad-spectrum antibiotics, which were mostly dispensed inappropriately. The National action plan of Pakistan on AMR should be implemented by policymakers including restrictions on the dispensing of antimicrobials.

Wastewater based environmental surveillance of toxigenic Vibrio cholerae in Pakistan

BACKGROUND

Pakistan has been experiencing intervals of sporadic cases and localized outbreaks in the last two decades. No proper study has been carried out in order to find out the environmental burden of toxigenic V. cholerae as well as how temporal and environmental factors associated in driving cholera across the country.

METHODS

We tested waste water samples from designated national environment surveillance sites in Pakistan with RT-PCR assay. Multistage sampling technique were utilized for samples collection and for effective sample processing Bag-Mediated Filtration system, were employed. Results were analysed by district and month wise to understand the geographic distribution and identify the seasonal pattern of V. cholera detection in Pakistan.

RESULTS

Between May 2019, and February 2020, we obtained and screened 160 samples in 12 districts across Pakistan. Out of 16 sentinel environmental surveillance sites, 15 sites showed positive results against cholera toxigenic gene with mostly lower CT value (mean, 34±2) and have significant difference (p < 0.05). The highest number of positive samples were collected from Sindh in month of November, then in June it is circulating in different districts of Pakistan including four Provinces respectively.

CONCLUSION

V. cholera detection do not follow a clear seasonal pattern. However, the poor sanitation problems or temperature and rainfall may potentially influence the frequency and duration of cholera across the country. Occurrence of toxigenic V. cholerae in the environment samples showed that cholera is endemic, which is an alarming for a potential future cholera outbreaks in the country.

Progress on the national action plan of Pakistan on antimicrobial resistance (AMR): a narrative review and the implications

Introduction: The emergence of antimicrobial resistance (AMR) is a threat to public health. In 2015, the World Health Organization (WHO) introduced a global action plan to tackle AMR in the World Health Assembly. Pakistan's national action plan (NAP) for AMR was released in May 2017 by the Ministry of National Health Services. Based on the NAP, strategies have been initiated on a national and provincial scale in Pakistan.Areas covered: This narrative review of the five components of the Pakistan NAP has been undertaken to discuss some of the challenges in implementation of the NAP for AMR in Pakistan including different opinions and views of key stakeholders, combined with suggestions on potential ways to reduce the burden of the AMR.Expert opinion: Going forward, healthcare authorities should focus on screening and monitoring of all the objectives of the NAP by establishing proper policies as well as promoting antimicrobial stewardship interventions and Infection prevention and control (IPC) practices. Overall, the comprehensive strengthening of the healthcare system is required to adequately implement the NAP, tackle continued inappropriate antimicrobial use and high AMR rates in Pakistan.

A Computational Systems Analyses to Identify Biomarkers and Mechanistic Link in Psoriasis and Cutaneous Squamous Cell Carcinoma

Psoriasis is the most common and chronic skin disease that affects individuals from every age group. The rate of psoriasis is increasing over the time in both developed and developing countries. Studies have revealed the possibility of association of psoriasis with skin cancers, particularly non-melanoma skin cancers (NMSC), which, include basal cell carcinoma and cutaneous squamous cell carcinoma (cSCC). There is a need to analyze the disease at molecular level to propose potential biomarkers and therapeutic targets in comparison to cSCC. Therefore, the second analyzed disease of this study is cSCC. It is the second most common prevalent skin cancer all over the world with the potential to metastasize and recur. There is an urge to validate the proposed biomarkers and discover new potential biomarkers as well. In order to achieve the goals and objectives of the study, microarray and RNA-sequencing data analyses were performed followed by network analysis. Afterwards, quantitative systems biology was implemented to analyze the results at a holistic level. The aim was to predict the molecular patterns that can lead psoriasis to cancer. The current study proposed potential biomarkers and therapeutic targets for psoriasis and cSCC. IL-17 signaling pathway is also identified as significant pathway in both diseases. Moreover, the current study proposed that autoimmune pathology, neutrophil recruitment, and immunity to extracellular pathogens are sensitive towards MAPKs (MAPK13 and MAPK14) and genes for AP-1 (FOSL1 and FOS). Therefore, these genes should be further studied in gene knock down based studies as they may play significant role in leading psoriasis towards cancer.

Enteral myiasis causing acute dysentery: A case report

Enteral myiasis or intestinal myiasis is acquired by ingesting food or water contaminated with dipteran fly eggs or larvae. Here, we describe a patient with intestinal myiasis presenting with acute dysentery caused by the larva of Hermetia illucens. The larva was identified morphologically, and its species confirmed through molecular analysis using polymerase chain reaction and sequencing based on mitochondrial cytochrome c oxidase subunit I gene (COI).

Complications of Sub-microscopic Plasmodium vivax Malaria among Orang Asli in Pos Lenjang, Kuala Lipis

In recent years, increasing cases of Plasmodium vivax complications had been reported all over the world. This former benign Plasmodium species is now recognized to be one of the human malaria parasites that can produce severe disease. In this article, we report two cases of sub-microscopic P. vivax malaria confirmed by PCR. Both patients were asymptomatic before treatment. They showed unusual presentations few days after initiation of antimalarial treatment. Both patients had subsequently completed antimalarial treatment and recovered completely.

Alterations of the salivary and fecal microbiome in patients with primary sclerosing cholangitis

BACKGROUND

Primary sclerosing cholangitis (PSC) is a chronic, progressive liver disease known for its frequent concurrence with inflammatory bowel disease. PSC can progress to cirrhosis, end-stage liver disease, hepatobiliary cancer, and/or colorectal cancer. The etiopathogenesis of PSC remains poorly understood, and, as such, pharmacotherapy has yet to be definitively established. Little is known about the salivary microbiome in PSC and PSC-IBD. This study aimed to evaluate the oral microbiome of patients with PSC, with association to these patient's fecal microbial composition.

METHODS

Saliva, fecal samples and Food Frequency Questionnaires were collected from 35 PSC patients with or without concomitant inflammatory bowel disease and 30 age- and BMI-matched healthy volunteers. 16S rRNA gene sequencing was performed using Illumina MiSeq platform.

RESULTS

The salivary microbial signature of PSC was significantly altered as compared to healthy controls, independent of concomitant IBD, and was comprised of 19 significantly altered species, of which, eight species were consistently overrepresented in both fecal and saliva of patients with PSC, including Veillonella, Scardovia and Streptococcus.

CONCLUSIONS

PSC is characterized by microbial dysbiosis in the gut and the salivary microbiome, independently from IBD. The PSC dysbiotic signature includes a reduction in autochthonous bacteria and an increased relative abundance of pathogenic bacteria, including an invasion of oral bacteria to the gut. PSC is a strong modulator of the microbial profile, in the gut and the oral microbiome. These results may lead to the development of biomarkers for screening and early diagnosis or the development of personalized medicine in PSC.

Biopsy outperforms reflectance confocal microscopy in diagnosing and subtyping basal cell carcinoma: results and experiences from a randomized controlled multicentre trial

Background

Reflectance confocal microscopy (RCM) is a noninvasive method for skin assessment, allowing entire lesion evaluation up to the papillary dermis. RCM is a potentially attractive alternative to punch biopsy (PB) in basal cell carcinoma (BCC).

Objectives

To determine the diagnostic accuracy of RCM vs. PB in diagnosing and subtyping BCC, and to study patient satisfaction and preferences.

Methods

Patients with a clinically suspected primary BCC were randomized between RCM and biopsy. Conventional surgical excision or follow‐up were used as reference. Sensitivity and specificity for BCC diagnosis and subtyping were calculated for both methods. BCC subtype was stratified based on clinical relevance: aggressive (infiltrative/micronodular) vs. nonaggressive (superficial/nodular) histopathological subtype and superficial vs. nonsuperficial BCC. Data on patient satisfaction and preferences were collected using a questionnaire and a contingent valuation method.

Results

Sensitivity for BCC diagnosis was high and similar for both methods (RCM 99·0% vs. biopsy 99·0%; P = 1·0). Specificity for BCC diagnosis was lower for RCM (59·1% vs. 100·0%; P < 0·001). Sensitivity for aggressive BCC subtypes was lower for RCM (33·3% vs. 77·3%; P = 0·003). Sensitivity for nonsuperficial BCC was not significantly different (RCM 88·9% vs. biopsy 91·0%; P = 0·724). Patient satisfaction and preferences were good and highly comparable for both methods.

Conclusions

Biopsy outperforms RCM in diagnosing and subtyping clinically suspected primary BCC. This outcome does not support routine clinical implementation of RCM, as a replacement for PBs in this patient group.

What is already known about this topic?

Expert groups have demonstrated the potency of in vivo diagnosing and subtyping of basal cell carcinoma (BCC) using confocal imaging. However, the diagnostic accuracy and financial consequences remain unclear, especially regarding correct subtyping.

What does this study add?

Confocal imaging was tested on performance in a real‐world clinical setting, as an alternative to diagnostic punch biopsies (PBs). In this setting, we concluded that for clinically suspicious primary BCC in daily practice, a PB remains preferred above confocal imaging, as it provides a superior accuracy for diagnosing and subtyping.

Linked Comment: Patalay. Br J Dermatol 2021; 184:590.

First case report of paragonimiasis in a Malaysian man

Paragonimiasis is an infection caused by Paragonimus, a lung fluke and is acquired by eating raw or undercooked crustaceans containing the infective metacercariae. Herein, we report a case of paragonimiasis in a Malaysian man who presented with incidental findings from chest radiographs. Examination of his biopsied lung tissue and sputum specimen revealed Paragonimus sp. eggs, whereas stool examination showed the presence of Giardia cysts. Patient was succesfully treated with praziquantel and metronidazole respectively.

Extended-spectrum beta-lactamases producing extensively drug-resistant Salmonella Typhi in Punjab, Pakistan

INTRODUCTION

The multidrug-resistant (MDR) Salmonella enterica serovar Typhi isolates have been increasingly reported from the Asian and African countries. The emergence of isolates with decreased susceptibility to fluoroquinolones and cephalosporins has worsened the situation. Recently, an outbreak from Sindh, Pakistan was reported caused by extensively drug-resistant (XDR) S. Typhi strains.

METHODOLOGY

In the present study, a total of 82 cases of typhoid have been investigated during 2018 from the febrile children referred to a tertiary care hospital in the population-wise largest province (Punjab) of Pakistan. S. Typhi was identified by standard microbiological techniques and isolates were characterized for antimicrobial resistance profiling and minimum inhibitory concentrations were determined. The presence of various ESBL genes in S. Typhi was confirmed by the PCR.

RESULTS

Out of the 82 isolates tested, 35 (43%) were found to be XDR; resistant to the first-line drugs. The resistance to third-generation cephalosporins was mainly mediated by extended-spectrum beta-lactamases i.e. blaTEM and blaCTX-M genes.

CONCLUSIONS

The higher prevalence of ESBL producing Salmonella typhi clinical strains raises the concern about transmission prevention and infection management in the community as well as clinical settings. Moreover, the study highlights the problem concerning the declining antibiotic arsenal for the therapeutic management of typhoid fever and the emergence and spread of XDR strains in Pakistan.

Publisher's Note: Glassy Dynamics in Disordered Electronic Systems Reveal Striking Thermal Memory Effects [Phys. Rev. Lett. 117, 116601 (2016)]

This corrects the article DOI: 10.1103/PhysRevLett.117.116601.

Glassy Dynamics in Disordered Electronic Systems Reveal Striking Thermal Memory Effects

Memory is one of the unique qualities of a glassy system. The relaxation of a glass to equilibrium contains information on the sample's excitation history, an effect often refer to as "aging." We demonstrate that under the right conditions a glass can also possess a different type of memory. We study the conductance relaxation of electron glasses that are fabricated at low temperatures. Remarkably, the dynamics are found to depend not only on the ambient measurement temperature but also on the maximum temperature to which the system was exposed. Hence the system "remembers" its highest temperature. This effect may be qualitatively understood in terms of energy barriers and local minima in configuration space and therefore may be a general property of the glass state.

Toxoplasmosis in HIV and non HIV prisoners in Malaysia

This is the first Malaysian study to determine the trend and risk factors of Toxoplasma gondii infection in HIV and non-HIV among prisoners in terms of socio-demographic and behavioural characteristics, clinical presentations and haematological distributions. Blood samples from 303 participants, comprising 133 HIV positive and 170 HIV negative inmates were collected in EDTA and plain tubes. Two mls of each blood sample in plain tubes were centrifuged at 1500 rpm for 10 minutes and the sera obtained were subjected to ELISA for detection of Toxoplasma IgM and IgG antibody towards Toxoplasma antigen. Seropositive samples for Toxoplasma IgM or both Toxoplasma IgM and IgG were further tested with Novalisa Toxoplasma gondii IgG avidity test to rule out acute from latent infections. Blood in EDTA tubes were sent to Clinical Diagnostic Lab (CDL), University Malaya Medical Centre (UMMC), Kuala Lumpur for complete blood count and differential count analysis. Overall seroprevalence of anti-T. gondii antibodies was detected in 41.9% (127 out of 303) of the participants. Anti-T. gondii antibodies was detected in 63.2% (84 out of 133) of HIV positive subjects and in 25.3% (43 out of 170) of HIV negative subjects. Seroprevalence of anti-T. gondii antibodies was significantly higher in HIV positive than in HIV negative subjects (OR = 5.06; 95% CI = 3.09-8.30; p < 0.001). The rate of T. gondii seropositivity increased significantly in those aged 40 years and above, HIV positive individuals and those with history of drug abuse. White blood cells (WBCs), neutrophils and basophils counts decreased significantly in those infected with Toxoplasma. Creating awareness about T. gondii infection and follow-up of their status is recommended. Moreover, screening of T. gondii infection in HIV-infected individuals should be considered for better treatment and management, including control and prevention.

The effect of phencyclidine on noradrenaline uptake by bovine chromaffin granules

The effects of the psychotomimetic drug, phencyclidine, on the reserpine sensitive uptake of (-)noradrenaline, on the reserpine resistant uptake of tryptamine, and on catecholamine release were studied in vitro using bovine chromaffin granules. Phencyclidine inhibited the uptake of (-)noradrenaline and tryptamine in a concentration-dependent manner. It caused 50% inhibition of (-)noradrenaline uptake at 2 X 10(-4)M and of tryptamine uptake at 7 X 10(-4)M. Release of catecholamines was not affected by phencyclidine at 0 degree C and pH 6--8 in concentrations up to 8 X 10(-3)M, whereas at 37 degrees C the drug (4 X 10(-3)M) caused a release that was increased when the pH was raised from 6 to 8. Since the effects of phencyclidine on chromaffin granule uptake and release are observed at high concentrations of the drug only, there is no evidence that these effects are relevant to the in vivo effects of the drug.

A case of acute kidney injury by near-drowning

Acute kidney injury following immersion or near-drowning is rarely described and no data from Malaysia have been found. We report a case of acute kidney injury following a near-drowning event. A 20-year-old man who recovered from near-drowning in a swimming pool 5 days earlier presented to our clinic with abdominal pain, anorexia, nausea and polyuria. Dipstick urinalysis showed a trace of blood. The serum creatinine level was 10-fold higher than the normal range. A bedside ultrasound showed features suggestive of acute tubular necrosis. He is then referred to the hospital with the diagnosis of acute kidney injury with the possibility of acute tubular necrosis secondary to near-drowning. We suggest that any patient presenting after immersion or near-drowning to be should assessed for potential acute kidney injury.

[Atopic dermatitis and prolonged exclusive breast-feeding]

BACKGROUND

We sought to compare the prevalence of exclusive breastfeeding throughout at least the first 6 months of life in patients presenting atopic dermatitis (AD) with a control group, and to check for a correlation between the duration of exclusive breastfeeding and the severity of AD.

PATIENTS AND METHODS

We conducted a case-control study with prospective inclusion over a period of 3 years. The study group consisted of 114 patients aged less than 15 years, from an urban area, presenting AD but with no personal or family history of atopy. Each patient was compared with two controls from the same town, matched for age and gender, with no personal or family history of atopy, and free of AD. Data analysis was performed using the SPSS software package, version 15.0. A P-value of less than 0.05 was considered as statistically significant.

RESULTS

The prevalence of exclusive breastfeeding for at least the first 6 months of life in the patient group was significantly lower than in the control group (P=0.0413). On the other hand, AD was significantly less severe in patients exclusively breastfed for longer than 9 months (P=0.0079).

CONCLUSION

The correlations recorded in our study do not allow us to draw any definite conclusions about a protective effect of exclusive breastfeeding with regard to AD. However, other benefits of extended exclusive breastfeeding justify supporting breastfeeding in a community with an existing sociocultural predisposition for this feeding method.

Characteristics of non-typhi Salmonella gastroenteritis associated with bacteremia in infants and young children

PURPOSE

To characterize the clinical and laboratory manifestations of non-typhi Salmonella gastroenteritis associated with bacteremia in children less than 36 months old.

METHODS

The study group included 17 patients, aged 2-34 months, with non-typhi Salmonella gastroenteritis and bacteremia, hospitalized in a tertiary pediatric medical center during the period 1995-2010. Clinical data were collected by medical chart review. Culture-related data were taken from the microbiology laboratory files. The results were compared with an assigned, age-matched, control group of 17 infants hospitalized with non-typhi Salmonella gastroenteritis without bacteremia.

RESULTS

Eleven cases (65%) occurred during the summer season. All patients presented with diarrhea, usually mixed with blood or mucus (clinical dysentery 65%). All but one had a high-grade fever (average 39.5°C). Three patients (19%) experienced convulsions during the acute episode of gastroenteritis. None of the patients had been previously treated with antibiotics. The most prevalent Salmonella serotype identified in the stool and blood was group C. Toxic appearance and convulsions on admission were more common among children with non-typhi Salmonella bacteremia, as opposed to those with non-typhi Salmonella gastroenteritis alone. No other epidemiological or laboratory differences were found.

CONCLUSIONS

Non-typhi Salmonella gastroenteritis poses a risk of bacteremia not only in infants younger than 3 months of age, but also in children younger than 36 months of age.

A community based study of Infant Mortality in rural Aligarh

BACKGROUND

Infant mortality rate is regarded as an important and sensitive indicator of the health status of a community. It also reflects the living standard of the people and the effectiveness of interventions for improving maternal and child health. Multiple factors related to social and economic conditions, health care and environment have a significant role to play on childhood mortality and improving childhood mortality is a national priority. The present study was planned to 1) determine the mortality rate among neonates and infants. 2) identification of pattern of various factors in relation to infant mortality and 3) to identify the causes of death in this age group.

METHOD

All the deaths in children under 12 months during July 2005 to June 2006 in Jawan block of district Aligarh, India were recorded. The cause of death was ascertained using the standard verbal autopsy procedure.

RESULTS

In the study period, 446 live births and 37 deaths in children under one year of age were reported. The neonatal and infant mortality rates were 49.4 and 83.0 per thousand live births respectively. The main causes of infant deaths were birth asphyxia, diarrhoea, pneumonia, prematurity (including Low birth weight and malnutrition).

CONCLUSION

Most of the death among infants are preventable, though promotion of institutional deliveries, strengthening of referral system, early recognition of danger signs and periodic retraining of health workers.

Shape-based Similarity Retrieval of Doppler Images for Clinical Decision Support

Flow Doppler imaging has become an integral part of an echocardiographic exam. Automated interpretation of flow doppler imaging has so far been restricted to obtaining hemodynamic information from velocity-time profiles depicted in these images. In this paper we exploit the shape patterns in Doppler images to infer the similarity in valvular disease labels for purposes of automated clinical decision support. Specifically, we model the similarity in appearance of Doppler images from the same disease class as a constrained non-rigid translation transform of the velocity envelopes embedded in these images. The shape similarity between two Doppler images is then judged by recovering the alignment transform using a variant of dynamic shape warping. Results of similarity retrieval of doppler images for cardiac decision support on a large database of images are presented.

Guidelines for the Pharmacological Treatment of Peripheral Neuropathic Pain: Expert Panel Recommendations for the Middle East Region

Neuropathic pain (NeP) has been the focus of extensive basic and clinical research over the past 20 years. This has led to an increased understanding of underlying pathophysiological mechanisms and the development of new therapeutic agents, as well as a clearer definition of the role of established medications. To date there are no published treatment guidelines for NeP in the Middle East. A multidisciplinary panel of Middle East and international experts met to review critically and reach a consensus on how best to apply evidence-based guidelines for the treatment of NeP (mainly peripheral NeP) in the Middle East. The expert panel recommended pregabalin, gabapentin and secondary amine tricyclic antidepressants (nortriptyline and desipramine) as first-line treatments for peripheral NeP. Serotonin-norepinephrine reuptake inhibitor antidepressants, tramadol and controlled-release opioid analgesics were recommended as second-line treatments. There is a need to increase diagnostic awareness of NeP, use validated screening questionnaires and undertake more treatment research in the Middle East region.