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3. Genomic analysis and in vivo efficacy of Pediococcus acidilactici as a potential probiotic to prevent hyperglycemia, hypercholesterolemia and gastrointestinal infections

Author

Al-Emran, Hassan M., Moon, Jannatul Ferdouse, Miah, Md. Liton, Meghla, Nigar Sultana, Reuben, Rine Christopher, Uddin, Mohammad Jashim, Ibnat, Habiba, Sarkar, Shovon Lal, Roy, Pravas Chandra, Rahman, M. Shaminur, Alam, A. S. M. Rubayet Ul, Islam, Ovinu Kibria, and Jahid, Iqbal Kabir

Published
2022
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6. A Multicountry Molecular Analysis of Salmonella enterica Serovar Typhi With Reduced Susceptibility to Ciprofloxacin in Sub-Saharan Africa

Author

Al-Emran, Hassan M., Eibach, Daniel, Krumkamp, Ralf, Ali, Mohammad, Baker, Stephen, Biggs, Holly M., Bjerregaard-Andersen, Morten, Breiman, Robert F., Clements, John D., Crump, John A., Espinoza, Ligia Maria Cruz, Deerin, Jessica, Dekker, Denise Myriam, Sow, Amy Gassama, Hertz, Julian T., Im, Justin, Ibrango, Samuel, von Kalckreuth, Vera, Kabore, Leon Parfait, Konings, Frank, Lefberg, Sandra Valborg, Meyer, Christian G., Mintz, Eric D., Montgomery, Joel M., Olack, Beatrice, Pak, Gi Deok, Panzner, Ursula, Park, Se Eun, Razafindrabe, Jean Luco Tsiriniaina, Rabezanahary, Henintsoa, Rakotondrainiarivelo, Jean Philibert, Rakotozandrindrainy, Raphaël, Raminosoa, Tiana Mirana, Schütt-Gerowitt, Heidi, Sampo, Emmanuel, Soura, Abdramane Bassiahi, Tall, Adama, Warren, Michelle, Wierzba, Thomas F., May, Jürgen, and Marks, Florian

Published
2016

7. The Emergence of Reduced Ciprofloxacin Susceptibility in Salmonella enterica Causing Bloodstream Infections in Rural Ghana

Author

Eibach, Daniel, Al-Emran, Hassan M., Dekker, Denise Myriam, Krumkamp, Ralf, Adu-Sarkodie, Yaw, Espinoza, Ligia Maria Cruz, Ehmen, Christa, Boahen, Kennedy, Heisig, Peter, Im, Justin, Jaeger, Anna, von Kalckreuth, Vera, Pak, Gi Deok, Panzner, Ursula, Park, Se Eun, Reinhardt, Alexander, Sarpong, Nimako, Schütt-Gerowitt, Heidi, Wierzba, Thomas F., Marks, Florian, and May, Jürgen

Published
2016

8. Validation and Identification of Invasive Salmonella Serotypes in Sub-Saharan Africa by Multiplex Polymerase Chain Reaction

Author

Al-Emran, Hassan M., Krumkamp, Ralf, Dekker, Denise Myriam, Eibach, Daniel, Aaby, Peter, Adu-Sarkodie, Yaw, Ali, Mohammad, Rubach, Mathew P., Bjerregaard-Andersen, Morten, Crump, John A., Espinoza, Ligia Maria Cruz, Lefberg, Sandra Valborg, Sow, Amy Gassama, Hertz, Julian T., Im, Justin, Jaeger, Anna, Kabore, Leon Parfait, Konings, Frank, Meyer, Christian G., Niang, Aissatou, Pak, Gi Deok, Panzner, Ursula, Park, Se Eun, Rabezanahary, Henintsoa, Rakotozandrindrainy, Raphaël, Raminosoa, Tiana Mirana, Razafindrabe, Tsiriniaina Jean Luco, Sampo, Emmanuel, Schütt-Gerowitt, Heidi, Sarpong, Nimako, Soura, Abdramane Bassiahi, Tall, Adama, von Kalckreuth, Vera, Wierzba, Thomas F., May, Jürgen, and Marks, Florian

Published
2016

9. Diagnosing Salmonella enterica Serovar Typhi Infections by Polymerase Chain Reaction Using EDTA Blood Samples of Febrile Patients From Burkina Faso

Author

Al-Emran, Hassan M., Hahn, Andreas, Baum, Jana, Espinoza, Ligia Maria Cruz, Deerin, Jessica, Im, Justin, Ibrango, Samuel, Kabore, Leon Parfait, von Kalckreuth, Vera, Konings, Frank, Marks, Florian, Sampo, Emmanuel, Panzner, Ursula, Park, Se Eun, Pak, Gi Deok, Schütt-Gerowitt, Heidi, Vinnemeier, Christof David, Warren, Michelle, and Soura, Abdramane Bassiahi

Published
2016

10. Variations of Invasive Salmonella Infections by Population Size in Asante Akim North Municipal, Ghana

Author

Espinoza, Ligia M., Nichols, Chelsea, Adu-Sarkodie, Yaw, Al-Emran, Hassan M., Baker, Stephen, Clemens, John D., Dekker, Denise Myriam, Eibach, Daniel, Krumkamp, Ralf, Boahen, Kennedy, Im, Justin, Jaeger, Anna, von Kalckreuth, Vera, Pak, Gi Deok, Panzner, Ursula, Park, Se Eun, Park, Jin Kyung, Sarpong, Nimako, Schütt-Gerowitt, Heidi, Toy, Trevor, Wierzba, Thomas F., Marks, Florian, and May, Jürgen

Published
2016

16. Dominant clade-featured SARS-CoV-2 co-occurring mutations reveals plausible epistasis: An in silico based hypothetical model

Author

Rubayet Ul Alam, A. S. M.; Islam, Ovinu Kibria; Hasan, Md. Shazid; Islam, Mir Raihanul; Mahmud, Shafi; Al-Emran, Hassan M.; Jahid, Iqbal Kabir; Crandall, Keith A.; Hossain, M. Anwar, http://orcid.org/0000-0003-2125-2218 Islam, Mir Raihanul, Rubayet Ul Alam, A. S. M.; Islam, Ovinu Kibria; Hasan, Md. Shazid; Islam, Mir Raihanul; Mahmud, Shafi; Al-Emran, Hassan M.; Jahid, Iqbal Kabir; Crandall, Keith A.; Hossain, M. Anwar, and http://orcid.org/0000-0003-2125-2218 Islam, Mir Raihanul

Abstract

PR, IFPRI3; ISI; DCA, PHND, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into eight fundamental clades with four of these clades (G, GH, GR, and GV) globally prevalent in 2020. To explain plausible epistatic effects of the signature co-occurring mutations of these circulating clades on viral replication and transmission fitness, we proposed a hypothetical model using in silico approach. Molecular docking and dynamics analyses showed the higher infectiousness of a spike mutant through more favorable binding of G614 with the elastase-2. RdRp mutation p.P323L significantly increased genome-wide mutations (p < 0.0001), allowing for more flexible RdRp (mutated)-NSP8 interaction that may accelerate replication. Superior RNA stability and structural variation at NSP3:C241T might impact protein, RNA interactions, or both. Another silent 5′-UTR:C241T mutation might affect translational efficiency and viral packaging. These four G-clade-featured co-occurring mutations might increase viral replication. Sentinel GH-clade ORF3a:p.Q57H variants constricted the ion-channel through intertransmembrane–domain interaction of cysteine(C81)-histidine(H57). The GR-clade N:p.RG203-204KR would stabilize RNA interaction by a more flexible and hypo-phosphorylated SR-rich region. GV-clade viruses seemingly gained the evolutionary advantage of the confounding factors; nevertheless, N:p.A220V might modulate RNA binding with no phenotypic effect. Our hypothetical model needs further retrospective and prospective studies to understand detailed molecular events and their relationship to the fitness of SARS-CoV-2.

Published
2022

17. Genomic analysis of SARS-CoV-2 variants of concern identified from the ChAdOx1 nCoV-19 immunized patients from southwest part of Bangladesh

Author

Al-Emran, Hassan M.; Hasan, Md. Shazid; Setu, Md. Ali Ahasan; Rahman, M. Shaminur; Ul Alam, Rubayet A. S. M.; Sarkar, Shovon Lal; Islam, Md. Tanvir; Islam, Mir Raihanul; Rahman, Mohammad Mahfuzur; Islam, Ovinu Kibria; Jahid, Iqbal Kabir; Hossain, M. Anwar, http://orcid.org/0000-0003-2125-2218 Islam, Mir Raihanul, Al-Emran, Hassan M.; Hasan, Md. Shazid; Setu, Md. Ali Ahasan; Rahman, M. Shaminur; Ul Alam, Rubayet A. S. M.; Sarkar, Shovon Lal; Islam, Md. Tanvir; Islam, Mir Raihanul; Rahman, Mohammad Mahfuzur; Islam, Ovinu Kibria; Jahid, Iqbal Kabir; Hossain, M. Anwar, and http://orcid.org/0000-0003-2125-2218 Islam, Mir Raihanul

Abstract

PR, IFPRI3; ISI; DCA; 5 Strengthening Institutions and Governance, PHND, Background Bangladesh introduced ChAdOx1 nCoV-19 since February, 2021 and in six months, only a small population (12.8%) received either one or two dose of vaccination like other low-income countries. The COVID-19 infections were continued to roll all over the places although the information on genomic variations of SARS-CoV-2 between both immunized and unimmunized group was unavailable. The objective of this study was to compare the proportion of immune escaping variants between those groups. Methods A total of 4718 nasopharygeal samples were collected from March 1 until April 15, 2021, of which, 834 (18%) were SARS-CoV-2 positive. The minimum sample size was calculated as 108 who were randomly selected for telephone interview and provided consent. The prevalence of SARS-CoV-2 variants and disease severity among both immunized and unimmunized groups was measured. A total of 63 spike protein sequences and 14 whole-genome sequences were performed from both groups and phylogenetic reconstruction and mutation analysis were compared. Results A total of 40 respondents (37%, N = 108) received single-dose and 2 (2%) received both doses of ChAdOx1 nCoV-19 vaccine, which significantly reduce dry cough, loss of appetite and difficulties in breathing compared to none. There was no significant difference in hospitalization, duration of hospitalization or reduction of other symptoms like running nose, muscle pain, shortness of breathing or generalized weakness between immunized and unimmunized groups. Spike protein sequence assumed 21 (87.5%) B.1.351, one B.1.526 and two 20B variants in immunized group compared to 27 (69%) B.1.351, 5 (13%) B.1.1.7, 4 (10%) 20B, 2 B.1.526 and one B.1.427 variant in unimmunized group. Whole genome sequence analysis of 14 cases identified seven B.1.351 Beta V2, three B.1.1.7 Alpha V1, one B.1.526 Eta and the rest three 20B variants. Conclusion Our study observed that ChAdOx1 could not prevent the new infection or severe COVID-19 disease outcome wit

Published
2022

19. Invasive Pneumococcal Disease among Children in Rural Bangladesh: Results from a Population-Based Surveillance

Author

Arifeen, Shams E., Saha, Samir K., Rahman, Sayedur, Rahman, Kazi Mizanur, Rahman, Syed Moshfiqur, Bari, Sanwarul, Naheed, Aliya, Mannan, Ishtiaq, Seraji, M. Habibur R., Ahmed, Nawshad U., Hassan, M. Shameem, Huda, Nazmul, Siddik, Ashraf Uddin, Quasem, Iftekhar, Islam, Maksuda, Fatima, Kaniz, Al-Emran, Hassan, Brooks, W. Abdullah, Baqui, Abdullah H., Breiman, Robert F., Sack, David, and Luby, Stephen P.

Published
2009
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22. Microbiome analysis revealing microbial interactions and secondary bacterial infections in COVID‐19 patients comorbidly affected by Type 2 diabetes.

Author

Al‐Emran, Hassan M., Rahman, Shaminur, Hasan, Md. Shazid, Ul Alam, Rubayet, Islam, Ovinu Kibria, Anwar, Ajwad, Jahid, Md. Iqbal K., and Hossain, Anwar

Subjects
SARS-CoV-2, COVID-19, BACTERIAL diseases, TYPE 2 diabetes, CARDIOVASCULAR diseases, LACTOBACILLUS rhamnosus
Abstract

The mortality of coronavirus disease 2019 (COVID‐19) disease is very high among the elderly or individuals having comorbidities such as obesity, cardiovascular diseases, lung infections, hypertension, and/or diabetes. Our study characterizes the metagenomic features in severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2)‐infected patients with or without type 2 diabetes, to identify the microbial interactions associated with its fatal consequences.This study compared the baseline nasopharyngeal microbiome of SARS‐CoV‐2‐infected diabetic and nondiabetic patients with controls adjusted for age and gender. The metagenomics based on next‐generation sequencing was performed using Ion GeneStudio S5 Series and the data were analyzed by the Vegan‐package in R. All three groups possessed significant bacterial diversity and dissimilarity indexes (p < 0.05). Spearman's correlation coefficient network analysis illustrated 183 significant positive correlations and 13 negative correlations of pathogenic bacteria (r = 0.6–1.0, p < 0.05), and 109 positive correlations between normal flora and probiotic bacteria (r > 0.6, p < 0.05). The SARS‐CoV‐2 diabetic group exhibited a significant increase in pathogens and secondary infection‐causing bacteria (p < 0.05) with a simultaneous decrease of normal flora (p < 0.05). The dysbiosis of the bacterial community might be linked with severe consequences of COVID‐19‐infected diabetic patients, although a few probiotic strains inhibited numerous pathogens in the same pathological niches. This study suggested that the promotion of normal flora and probiotics through dietary supplementation and excessive inflammation reduction by preventing secondary infections might lead to a better outcome for those comorbid patients. [ABSTRACT FROM AUTHOR]

Published
2023
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23. Initial reports of the SARS‐CoV ‐2 Delta variant (B.1.617.2 lineage) in Bangladeshi patients: Risks of cross‐border transmission from India

Author

Hasan, Md. Shazid, primary, Islam, Md. Tanvir, additional, Alam, A. S. M. Rubayet Ul, additional, Sarkar, Shovon Lal, additional, Rahman, M. Shaminur, additional, Islam, Ovinu Kibria, additional, Setu, Md. Ali Ahsan, additional, Chakrovarty, Tanay, additional, Al‐Emran, Hassan M., additional, Jahid, Iqbal Kabir, additional, and Hossain, M. Anwar, additional

Published
2021
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24. Genomic analysis of SARS-CoV-2 variants of concern identified from the ChAdOx1 nCoV-19 immunized patients from Southwest part of Bangladesh

Author

Al-Emran, Hassan M., primary, Hasan, Md. Shazid, additional, Setu, Md. Ali Ahsan, additional, Rahman, Md. Shaminur, additional, Alam, ASM Rubayet Ul, additional, Sarkar, Shovon Lal, additional, Islam, Md. Tanvir, additional, Islam, Mir Raihanul, additional, Rahman, Mohammad Mahfuzur, additional, Islam, Ovinu Kibria, additional, Jahid, Iqbal Kabir, additional, and Hossain, M. Anwar, additional

Published
2021
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27. A rapid and cost‐effective multiplex ARMS‐PCR method for the simultaneous genotyping of the circulating SARS‐CoV‐2 phylogenetic clades

Author

Islam, Mohammad Tanvir, primary, Alam, ASM Rubayet Ul, additional, Sakib, Najmuj, additional, Hasan, Mohammad Shazid, additional, Chakrovarty, Tanay, additional, Tawyabur, Mohammad, additional, Islam, Ovinu Kibria, additional, Al‐Emran, Hassan M., additional, Jahid, Mohammad Iqbal Kabir, additional, and Anwar Hossain, Mohammad, additional

Published
2021
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29. Dominant clade‐featured SARS‐CoV‐2 co‐occurring mutations reveal plausible epistasis: An in silico based hypothetical model.

Author

Alam, A. S. M. Rubayet Ul, Islam, Ovinu Kibria, Hasan, Md. Shazid, Islam, Mir Raihanul, Mahmud, Shafi, Al‐Emran, Hassan M., Jahid, Iqbal Kabir, Crandall, Keith A., and Hossain, M. Anwar

Subjects
SARS-CoV-2, GENETIC mutation, VIRAL transmission
Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has evolved into eight fundamental clades with four of these clades (G, GH, GR, and GV) globally prevalent in 2020. To explain plausible epistatic effects of the signature co‐occurring mutations of these circulating clades on viral replication and transmission fitness, we proposed a hypothetical model using in silico approach. Molecular docking and dynamics analyses showed the higher infectiousness of a spike mutant through more favorable binding of G614 with the elastase‐2. RdRp mutation p.P323L significantly increased genome‐wide mutations (p < 0.0001), allowing for more flexible RdRp (mutated)‐NSP8 interaction that may accelerate replication. Superior RNA stability and structural variation at NSP3:C241T might impact protein, RNA interactions, or both. Another silent 5′‐UTR:C241T mutation might affect translational efficiency and viral packaging. These four G‐clade‐featured co‐occurring mutations might increase viral replication. Sentinel GH‐clade ORF3a:p.Q57H variants constricted the ion‐channel through intertransmembrane–domain interaction of cysteine(C81)‐histidine(H57). The GR‐clade N:p.RG203‐204KR would stabilize RNA interaction by a more flexible and hypo‐phosphorylated SR‐rich region. GV‐clade viruses seemingly gained the evolutionary advantage of the confounding factors; nevertheless, N:p.A220V might modulate RNA binding with no phenotypic effect. Our hypothetical model needs further retrospective and prospective studies to understand detailed molecular events and their relationship to the fitness of SARS‐CoV‐2. Highlights: Most dominant spike mutation favors elastase‐2 binding.The polymerase mutant (P323L) virus may speed up replication that corresponds to higher mutations.ORF3a viroporin substitution (Q57H) decreases ion permeability.N protein mutation (RG203‐204KR) can increase nucleocapsid stability and help evade immunity.Co‐occurring mutations might modulate viral replication and transmission fitness through epistasis. [ABSTRACT FROM AUTHOR]

Published
2022
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30. A rapid and cost-effective multiplex ARMS-PCR method for the simultaneous genotyping of the circulating SARS-CoV-2 phylogenetic clades

Author

Islam, Md. Tanvir, primary, Alam, A. S. M. Rubayet Ul, additional, Sakib, Najmuj, additional, Hasan, Md. Shazid, additional, Chakrovarty, Tanay, additional, Tawyabur, Md., additional, Islam, Ovinu Kibria, additional, Al-Emran, Hassan M., additional, Jahid, Iqbal Kabir, additional, and Hossain, M. Anwar, additional

Published
2020
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33. Malaria Coinfections in Febrile Pediatric Inpatients: A Hospital-Based Study From Ghana

Author

Hogan, Benedikt, Eibach, Daniel, Krumkamp, Ralf, Sarpong, Nimako, Dekker, Denise, Kreuels, Benno, Maiga-Ascofaré, Oumou, Gyau Boahen, Kennedy, Wiafe Akenten, Charity, Adu-Sarkodie, Yaw, Owusu-Dabo, Ellis, May, Jürgen, Ammer, Luise, Struck, Nicole, Hahn, Andreas, Herr, Wiebke, Jaeger, Anna, Levermann, Vinzent, Loag, Wibke, Mertens, Eva, Reigl, Lisa, Steierberg, Stefanie, Winter, Doris, Al-Emran, Hassan, Boateng, Harry Owusu, Rettig, Theresa, Binger, Tabea, Hanson, Henry, Oppong, Kwabena, Nagel, Michael, Aepfelbacher, Martin, Buehl, Henrike, Henrichfreise, Beate, Cadar, Daniel, Eckerle, Isabella, Drosten, Christian, Ittrich, Harald, Tannich, Egbert, Thielebei, Anke, and Eckerle, Isabella Anne

Subjects
0301 basic medicine, Male, Gastrointestinal Diseases, Parasitemia, medicine.disease_cause, Ghana, Parasite Load, Malaria/epidemiology/microbiology/virology, 0302 clinical medicine, Cost of Illness, Rotavirus, Epidemiology, Prospective Studies, Child, Urinary Tract Infections/epidemiology/microbiology, Articles and Commentaries, Respiratory Tract Infections, fever, Respiratory tract infections, Coinfection, Hospitalization, Infectious Diseases, Child, Preschool, Urinary Tract Infections, Female, Fever/etiology/parasitology, Microbiology (medical), medicine.medical_specialty, Adolescent, 030231 tropical medicine, malaria, 03 medical and health sciences, children, Internal medicine, Streptococcus pneumoniae, parasitic diseases, medicine, Coinfection/epidemiology, Humans, Gastrointestinal Diseases/epidemiology/virology, Ghana/epidemiology, Respiratory Tract Infections/epidemiology/microbiology, business.industry, Infant, medicine.disease, Parasitemia/epidemiology, Pneumonia, 030104 developmental biology, Africa, business, Malaria
Abstract

In malaria patients admitted to the study hospital, the likelihood of a co-diagnosis decreased with an increasing parasite count. In malaria-endemic settings, parasite densities provide important information for patient management, in particular for antimicrobial medication., Background The epidemiology of pediatric febrile illness is shifting in sub-Saharan Africa, but malaria remains a major cause of childhood morbidity and mortality. The present study describes causes of febrile illness in hospitalized children in Ghana and aims to determine the burden of malaria coinfections and their association with parasite densities. Methods In a prospective study, children (aged ≥30 days and ≤15 years) with fever ≥38.0°C were recruited after admission to the pediatric ward of a primary hospital in Ghana. Malaria parasitemia was determined and blood, stool, urine, respiratory, and cerebrospinal fluid specimens were screened for parasitic, bacterial, and viral pathogens. Associations of Plasmodium densities with other pathogens were calculated. Results From November 2013 to April 2015, 1238 children were enrolled from 4169 admissions. A clinical/microbiological diagnosis could be made in 1109/1238 (90%) patients, with Plasmodium parasitemia (n = 728/1238 [59%]) being predominant. This was followed by lower respiratory tract infections/pneumonia (n = 411/1238 [34%]; among detected pathogens most frequently Streptococcus pneumoniae, n = 192/299 [64%]), urinary tract infections (n = 218/1238 [18%]; Escherichia coli, n = 21/32 [66%]), gastrointestinal infections (n = 210 [17%]; rotavirus, n = 32/97 [33%]), and invasive bloodstream infections (n = 62 [5%]; Salmonella species, n = 47 [76%]). In Plasmodium-infected children the frequency of lower respiratory tract, gastrointestinal, and bloodstream infections increased with decreasing parasite densities. Conclusions In a hospital setting, the likelihood of comorbidity with a nonmalarial disease is inversely correlated with increasing blood levels of malaria parasites. Hence, parasite densities provide important information as an indicator for the probability of coinfection, in particular to guide antimicrobial medication.

Published
2018

34. Emergence of phylogenetically diverse and fluoroquinolone resistant Salmonella Enteritidis as a cause of invasive nontyphoidal Salmonella disease in Ghana

Author

Aldrich, Cassandra, primary, Hartman, Hassan, additional, Feasey, Nicholas, additional, Chattaway, Marie Anne, additional, Dekker, Denise, additional, Al-Emran, Hassan M., additional, Larkin, Lesley, additional, McCormick, Jacquelyn, additional, Sarpong, Nimako, additional, Le Hello, Simon, additional, Adu-Sarkodie, Yaw, additional, Panzner, Ursula, additional, Park, Se Eun, additional, Im, Justin, additional, Marks, Florian, additional, May, Jürgen, additional, Dallman, Timothy J., additional, and Eibach, Daniel, additional

Published
2019
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35. Emergence of European and North American mutant variants of SARS‐CoV‐2 in South‐East Asia.

Author

Islam, Ovinu Kibria, Al‐Emran, Hassan M., Hasan, Md. Shazid, Anwar, Azraf, Jahid, Md. Iqbal Kabir, and Hossain, Md. Anwar

Subjects
*SARS-CoV-2, *COVID-19 pandemic, *COVID-19, *VIRAL mutation, *HIGH temperatures, *PHYLOGEOGRAPHY
Abstract

The SARS‐CoV‐2 coronavirus is responsible for the current COVID‐19 pandemic, with an ongoing toll of over 5 million infections and 333 thousand deaths worldwide within the first 5 months. Insight into the phylodynamics and mutation variants of this virus is vital to understanding the nature of its spread in different climate conditions. The incidence rate of COVID‐19 is increasing at an alarming pace within subtropical South‐East Asian nations with high temperatures and humidity. To understand this spread, we analysed 444 genome sequences of SARS‐CoV‐2 available on the GISAID platform from six South‐East Asian countries. Multiple sequence alignments and maximum‐likelihood phylogenetic analyses were performed to analyse and characterize the non‐synonymous (NS) mutant variants circulating in this region. Global mutation distribution analysis showed that the majority of the mutations found in this region are also prevalent in Europe and North America, and the concurrent presence of these mutations at a high frequency in other countries indicates possible transmission routes. Unique spike protein and non‐structural protein mutations were observed circulating within confined area of a given country. We divided the circulating viral strains into four major groups and three subgroups on the basis of the most frequent NS mutations. Strains with a unique set of four co‐evolving mutations were found to be circulating at a high frequency within India, specifically. Group 2 strains characterized by two co‐evolving NS mutants which alter in RdRp (P323L) and spike (S) protein (D614G) were found to be common in Europe and North America. These European and North American variants have rapidly emerged as dominant strains within South‐East Asia, increasing from a 0% prevalence in January to an 81% by May 2020. These variants may have an evolutionary advantage over their ancestral types and could present a large threat to South‐East Asia for the coming winter. [ABSTRACT FROM AUTHOR]

Published
2021
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36. Prevalence of nasal colonisation by methicillin-sensitive and methicillin-resistant Staphylococcus aureus among healthcare workers and students in Madagascar

Author

Hogan, Benedikt, Rakotozandrindrainy, Raphael, Dekker, Denise, Jaeger, Anna, Poppert, Sven, Frickmann, Hagen, Micheel, Volker, Crusius, Sabine, Heriniaina, Jean Noel, Rakotondrainiarivelo, Jean Philibert, Razafindrabe, Tsiriniaina, May, Jürgen, Schwarz, Norbert Georg, and Al-Emran, Hassan

Subjects
biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses
Abstract

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) clones pose a significant threat to hospitalised patients because the bacteria can be transmitted by asymptomatic carriers within healthcare facilities. To date, nothing is known about the prevalence of S. aureus and MRSA among healthcare workers in Madagascar. The objective of our study was to examine the prevalence and clonal epidemiology of nasal S. aureus and MRSA among healthcare workers and non-medical University students in Antananarivo, Madagascar. METHODS: This cross sectional study screened nasal swabs taken from students and healthcare workers for S. aureus. Multiplex PCR was performed to identify S. aureus-specific (nuc), MRSA-specific mecA and mecC genes, Panton-Valentine leukocidin (PVL) (lukF-PV), and toxic shock syndrome toxin-1 (TSST-1) specific genes in methicillin-sensitive S. aureus (MSSA) and MRSA isolates. Staphylococcus protein A gene (spa) typing was performed for all confirmed MRSA isolates. The frequency distribution of nasal S. aureus and MRSA of healthcare workers and non-medical students was compared using Pearson’s χ2 test. RESULTS: Of 1548 nasal swabs tested, 171 (11 %) were positive for S. aureus; 20 (1.3 %) of these isolates were identified as MRSA. S. aureus was detected in 91 of 863 healthcare workers (10.4 %) and in 80 (11.8 %) of 685 students; however, 14 (1.5 %) healthcare workers carried MRSA compared with six (0.9 %) students. Nasal carriage of S. aureus and MRSA was more prevalent in women than in men, and 21 (11.7 %) S. aureus isolates were PVL-positive and 36 (21 %) were TSST-1 positive. The mecC gene was not detected in any isolates. Five different spa types were identified, with spa type t186 being the predominant MRSA clone (16/20). CONCLUSION: The results of the present study reveal a low frequency of S. aureus and MRSA nasal carriage in both students and healthcare workers from Antananarivo, Madagascar. The predominant MRSA clone (t186) was previously described in hospitalised patients in Madagascar.

Published
2016

37. Additional file 1: of Prevalence of nasal colonisation by methicillin-sensitive and methicillin-resistant Staphylococcus aureus among healthcare workers and students in Madagascar

Author

Hogan, Benedikt, Rakotozandrindrainy, Raphael, Al-Emran, Hassan, Dekker, Denise, Hahn, Andreas, Jaeger, Anna, Poppert, Sven, Frickmann, Hagen, Hagen, Ralf, Micheel, Volker, Crusius, Sabine, Heriniaina, Jean, Rakotondrainiarivelo, Jean, Tsiriniaina Razafindrabe, JĂźrgen May, and Schwarz, Norbert

Abstract

Supporting Information Table S1. Primers used for PCR screening of nasal S. aureus isolates obtained from Madagascan students and healthcare workers. (PDF 73Â kb)

Published
2016
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38. Variations of Invasive Salmonella Infections by Population Size in Asante Akim North Municipal, Ghana

Author

Espinoza, Ligia M. Cruz, Nichols, Chelsea, Adu-Sarkodie, Yaw, Al-Emran, Hassan M., Baker, Stephen, Clemens, John D., Dekker, Denise Myriam, Eibach, Daniel, Krumkamp, Ralf, Boahen, Kennedy, Im, Justin, Jaeger, Anna, von Kalckreuth, Vera, Pak, Gi Deok, Panzner, Ursula, Park, Se Eun, Park, Jin Kyung, Sarpong, Nimako, Schuett-Gerowitt, Heidi, Toy, Trevor, Wierzba, Thomas F., Marks, Florian, May, Juergen, Espinoza, Ligia M. Cruz, Nichols, Chelsea, Adu-Sarkodie, Yaw, Al-Emran, Hassan M., Baker, Stephen, Clemens, John D., Dekker, Denise Myriam, Eibach, Daniel, Krumkamp, Ralf, Boahen, Kennedy, Im, Justin, Jaeger, Anna, von Kalckreuth, Vera, Pak, Gi Deok, Panzner, Ursula, Park, Se Eun, Park, Jin Kyung, Sarpong, Nimako, Schuett-Gerowitt, Heidi, Toy, Trevor, Wierzba, Thomas F., Marks, Florian, and May, Juergen

Abstract

Methods.aEuro integral Children recruited at the Agogo Presbyterian Hospital and meeting TSAP inclusion criteria were included in the analysis. Towns with > 32 000 inhabitants were considered urban; towns with populations < 5200 were considered rural. Adjusted IRs for Salmonella bloodstream infections were estimated for both settings. Setting-specific age-standardized incidence rates for children aged < 15 years were derived and used to calculate age-standardized rate ratios (SRRs) to evaluate differences between settings. Results.aEuro integral Eighty-eight percent (2651/3000) of recruited patients met inclusion criteria and were analyzed. IRs of Salmonella bloodstream infections in children < 15 years old were > 100 per 100 000 PYO in both settings. Among rural children, the Salmonella Typhi and iNTS rates were 2 times (SRR, 2.2; 95% confidence interval [CI], 1.3-3.5) and almost 3 times (SRR, 2.8; 95% CI, 1.9-4.3) higher, respectively, than rates in urban children. Conclusions. IRs of Salmonella bloodstream infections in children < 15 years old in AAN, Ghana, differed by setting, with 2 to nearly 3 times higher rates in the less populated setting. Variations in the distribution of the disease should be considered to implement future studies and intervention strategies.

Published
2016

39. Prevalence of nasal colonisation by methicillin-sensitive and methicillin-resistant Staphylococcus aureus among healthcare workers and students in Madagascar

Author

Hogan, Benedikt, primary, Rakotozandrindrainy, Raphael, additional, Al-Emran, Hassan, additional, Dekker, Denise, additional, Hahn, Andreas, additional, Jaeger, Anna, additional, Poppert, Sven, additional, Frickmann, Hagen, additional, Hagen, Ralf Matthias, additional, Micheel, Volker, additional, Crusius, Sabine, additional, Heriniaina, Jean Noel, additional, Rakotondrainiarivelo, Jean Philibert, additional, Razafindrabe, Tsiriniaina, additional, May, Jürgen, additional, and Schwarz, Norbert Georg, additional

Published
2016
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40. DiagnosingSalmonella entericaSerovar Typhi Infections by Polymerase Chain Reaction Using EDTA Blood Samples of Febrile Patients From Burkina Faso

Author

Al-Emran, Hassan M., primary, Hahn, Andreas, additional, Baum, Jana, additional, Cruz Espinoza, Ligia Maria, additional, Deerin, Jessica, additional, Im, Justin, additional, Ibrango, Samuel, additional, Kabore, Leon Parfait, additional, von Kalckreuth, Vera, additional, Konings, Frank, additional, Marks, Florian, additional, Sampo, Emmanuel, additional, Panzner, Ursula, additional, Park, Se Eun, additional, Pak, Gi Deok, additional, Schütt-Gerowitt, Heidi, additional, Vinnemeier, Christof David, additional, Warren, Michelle, additional, and Soura, Abdramane Bassiahi, additional

Published
2016
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41. The Emergence of Reduced Ciprofloxacin Susceptibility inSalmonella entericaCausing Bloodstream Infections in Rural Ghana

Author

Eibach, Daniel, primary, Al-Emran, Hassan M., additional, Dekker, Denise Myriam, additional, Krumkamp, Ralf, additional, Adu-Sarkodie, Yaw, additional, Cruz Espinoza, Ligia Maria, additional, Ehmen, Christa, additional, Boahen, Kennedy, additional, Heisig, Peter, additional, Im, Justin, additional, Jaeger, Anna, additional, von Kalckreuth, Vera, additional, Pak, Gi Deok, additional, Panzner, Ursula, additional, Park, Se Eun, additional, Reinhardt, Alexander, additional, Sarpong, Nimako, additional, Schütt-Gerowitt, Heidi, additional, Wierzba, Thomas F., additional, Marks, Florian, additional, and May, Jürgen, additional

Published
2016
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42. A Multicountry Molecular Analysis ofSalmonella entericaSerovar Typhi With Reduced Susceptibility to Ciprofloxacin in Sub-Saharan Africa

Author

Al-Emran, Hassan M., primary, Eibach, Daniel, additional, Krumkamp, Ralf, additional, Ali, Mohammad, additional, Baker, Stephen, additional, Biggs, Holly M., additional, Bjerregaard-Andersen, Morten, additional, Breiman, Robert F., additional, Clemens, John D., additional, Crump, John A., additional, Cruz Espinoza, Ligia Maria, additional, Deerin, Jessica, additional, Dekker, Denise Myriam, additional, Gassama Sow, Amy, additional, Hertz, Julian T., additional, Im, Justin, additional, Ibrango, Samuel, additional, von Kalckreuth, Vera, additional, Kabore, Leon Parfait, additional, Konings, Frank, additional, Løfberg, Sandra Valborg, additional, Meyer, Christian G., additional, Mintz, Eric D., additional, Montgomery, Joel M., additional, Olack, Beatrice, additional, Pak, Gi Deok, additional, Panzner, Ursula, additional, Park, Se Eun, additional, Razafindrabe, Jean Luco Tsiriniaina, additional, Rabezanahary, Henintsoa, additional, Rakotondrainiarivelo, Jean Philibert, additional, Rakotozandrindrainy, Raphaël, additional, Raminosoa, Tiana Mirana, additional, Schütt-Gerowitt, Heidi, additional, Sampo, Emmanuel, additional, Soura, Abdramane Bassiahi, additional, Tall, Adama, additional, Warren, Michelle, additional, Wierzba, Thomas F., additional, May, Jürgen, additional, and Marks, Florian, additional

Published
2016
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43. Variations of InvasiveSalmonellaInfections by Population Size in Asante Akim North Municipal, Ghana

Author

Cruz Espinoza, Ligia M., primary, Nichols, Chelsea, additional, Adu-Sarkodie, Yaw, additional, Al-Emran, Hassan M., additional, Baker, Stephen, additional, Clemens, John D., additional, Dekker, Denise Myriam, additional, Eibach, Daniel, additional, Krumkamp, Ralf, additional, Boahen, Kennedy, additional, Im, Justin, additional, Jaeger, Anna, additional, von Kalckreuth, Vera, additional, Pak, Gi Deok, additional, Panzner, Ursula, additional, Park, Se Eun, additional, Park, Jin Kyung, additional, Sarpong, Nimako, additional, Schütt-Gerowitt, Heidi, additional, Toy, Trevor, additional, Wierzba, Thomas F., additional, Marks, Florian, additional, and May, Jürgen, additional

Published
2016
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44. Detection of a NovelgyrBMutation Associated With Fluoroquinolone-NonsusceptibleSalmonella entericaserovar Typhimurium Isolated From a Bloodstream Infection in Ghana

Author

Al-Emran, Hassan M., primary, Heisig, Anke, additional, Dekker, Denise, additional, Adu-Sarkodie, Yaw, additional, Cruz Espinoza, Ligia Maria, additional, Panzner, Ursula, additional, von Kalckreuth, Vera, additional, Marks, Florian, additional, Park, Se Eun, additional, Sarpong, Nimako, additional, May, Jürgen, additional, and Heisig, Peter, additional

Published
2016
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45. Validation and Identification of InvasiveSalmonellaSerotypes in Sub-Saharan Africa by Multiplex Polymerase Chain Reaction: Table 1.

Author

Al-Emran, Hassan M., primary, Krumkamp, Ralf, additional, Dekker, Denise Myriam, additional, Eibach, Daniel, additional, Aaby, Peter, additional, Adu-Sarkodie, Yaw, additional, Ali, Mohammad, additional, Rubach, Mathew P., additional, Bjerregaard-Andersen, Morten, additional, Crump, John A., additional, Cruz Espinoza, Ligia Maria, additional, Løfberg, Sandra Valborg, additional, Gassama Sow, Amy, additional, Hertz, Julian T., additional, Im, Justin, additional, Jaeger, Anna, additional, Kabore, Leon Parfait, additional, Konings, Frank, additional, Meyer, Christian G., additional, Niang, Aissatou, additional, Pak, Gi Deok, additional, Panzner, Ursula, additional, Park, Se Eun, additional, Rabezanahary, Henintsoa, additional, Rakotozandrindrainy, Raphaël, additional, Raminosoa, Tiana Mirana, additional, Razafindrabe, Tsiriniaina Jean Luco, additional, Sampo, Emmanuel, additional, Schütt-Gerowitt, Heidi, additional, Sarpong, Nimako, additional, Soura, Abdramane Bassiahi, additional, Tall, Adama, additional, von Kalckreuth, Vera, additional, Wierzba, Thomas F., additional, May, Jürgen, additional, and Marks, Florian, additional

Published
2016
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46. Population-based Incidence and Etiology of Community-acquired Neonatal Viral Infections in Bangladesh

Author

Farzin, Azadeh, primary, Saha, Samir K., additional, Baqui, Abdullah H., additional, Choi, Yoonjoung, additional, Ahmed, Nawshad Uddin, additional, Simoes, Eric A.F., additional, El Arifeen, Shams, additional, Al-Emran, Hassan M., additional, Bari, Sanwarul, additional, Rahman, Syed M., additional, Mannan, Ishtiaq, additional, Crook, Derrick, additional, Seraji, Habibur Rahman, additional, Begum, Nazma, additional, Black, Robert E., additional, Santosham, Mathuram, additional, and Darmstadt, Gary L., additional

Published
2015
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49. Variations of Invasive Salmonella Infections by Population Size in Asante Akim North Municipal, Ghana.

Author

Cruz Espinoza, Ligia M., Nichols, Chelsea, Adu-Sarkodie, Yaw, Al-Emran, Hassan M., Baker, Stephen, Clemens, John D., Dekker, Denise Myriam, Eibach, Daniel, Krumkamp, Ralf, Boahen, Kennedy, Im, Justin, Jaeger, Anna Jaeger, von Kalckreuth, Vera, Gi Deok Pak, Panzner, Ursula, Se Eun Park, Jin Kyung Park, Sarpong, Nimako, Schütt-Gerowitt, Heidi, and Toy, Trevor

Abstract

Background. The Typhoid Fever Surveillance in Africa Program (TSAP) estimated adjusted incidence rates (IRs) for Salmonella enterica serovar Typhi and invasive nontyphoidal S. enterica serovars (iNTS) of >100 cases per 100 000 person-years of observation (PYO) for children aged <15 years in Asante Akim North Municipal (AAN), Ghana, between March 2010 and May 2012. We analyzed how much these rates differed between rural and urban settings. Methods. Children recruited at the Agogo Presbyterian Hospital and meeting TSAP inclusion criteria were included in the analysis. Towns with >32 000 inhabitants were considered urban; towns with populations <5200 were considered rural. Adjusted IRs for Salmonella bloodstream infections were estimated for both settings. Setting-specific age-standardized incidence rates for children aged <15 years were derived and used to calculate age-standardized rate ratios (SRRs) to evaluate differences between settings. Results. Eighty-eight percent (2651/3000) of recruited patients met inclusion criteria and were analyzed. IRs of Salmonella bloodstream infections in children <15 years old were >100 per 100 000 PYO in both settings. Among rural children, the Salmonella Typhi and iNTS rates were 2 times (SRR, 2.2; 95% confidence interval [CI], 1.3–3.5) and almost 3 times (SRR, 2.8; 95% CI, 1.9–4.3) higher, respectively, than rates in urban children. Conclusions. IRs of Salmonella bloodstream infections in children <15 years old in AAN, Ghana, differed by setting, with 2 to nearly 3 times higher rates in the less populated setting. Variations in the distribution of the disease should be considered to implement future studies and intervention strategies. [ABSTRACT FROM AUTHOR]

Published
2016
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