Sharmin Jamshid Baig

SARS-CoV-2 sequencing artifacts associated with targeted PCR enrichment and read mapping

Kirsten Ellegaard, Vithiagaran Gunalan, Raphael Niklaus Sieber, Sharmin Jamshid Baig et autres

Protocols and pipelines for SARS-CoV-2 genome sequencing were rapidly established when the COVID-19 outbreak was declared a pandemic. The most widely used approach for sequencing SARS-CoV-2 includes targeted enrichment by PCR, followed by shotgun sequencing and reference-based genome assembly. As the continued …

dk, au (code pays fourni par la source)

Genomic Epidemiology of Clonal Complex 1 Staphylococcus aureu s in Remote Western Australian Communities

Nicholas W.T. Yee, Geoffrey Wallace Coombs, Marc Stegger, Sharmin Jamshid Baig et autres

Community‐associated methicillin‐resistant Staphylococcus aureus (CA‐MRSA) was first reported in Western Australia (WA) in the 1990s. Although ST8‐IVa [2B] (WA‐5) was the first identified CA‐MRSA in WA, ST1‐IVa [2B] (WA‐1) soon emerged as the dominant clone. To investigate the genomic epidemiology of clonal …

au, dk (code pays fourni par la source)

SARS-CoV-2 sequencing artifacts associated with targeted PCR enrichment and read mapping

Kirsten Ellegaard, Vithiagaran Gunalan, Raphael Niklaus Sieber, Sharmin Jamshid Baig et autres

Abstract Protocols and pipelines for SARS-CoV-2 genome sequencing were rapidly established when the COVID-19 outbreak was declared a pandemic. The most widely used approach for sequencing SARS-CoV-2 includes targeted enrichment by PCR, followed by shotgun sequencing and reference-based genome assembly. As the …

dk, gb, au (code pays fourni par la source)

Virus isolation and neutralisation of SARS-CoV-2 variants BA.2.86 and EG.5.1

Ria Lassaunière, Charlotta Polacek, Magdalena Utko, Karina Medin Sorensen et autres

dk, us, fr, au (code pays fourni par la source)

Neutralisation of SARS-CoV-2 Omicron subvariants BA.2.86 and EG.5.1 by antibodies induced by earlier infection or vaccination

Ria Lassaunière, Charlotta Polacek, Sharmin Jamshid Baig, Kirsten Ellegaard et autres

Abstract Highly mutated SARS-CoV-2 Omicron subvariant BA.2.86 emerged in July 2023. We investigated the neutralisation of isolated virus by antibodies induced by earlier infection or vaccination. The neutralisation titres for BA.2.86 were comparable to those for XBB.1 and EG.5.1, by antibodies induced …

dk, fr, au (code pays fourni par la source)

First cases of SARS-CoV-2 BA.2.86 in Denmark, 2023

Morten Rasmussen, Frederik Trier Møller, Vithiagaran Gunalan, Sharmin Jamshid Baig et autres

We describe 10 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant BA.2.86 detected in Denmark, including molecular characteristics and results from wastewater surveillance that indicate that the variant is circulating in the country at a low level. This new variant …

dk, au (code pays fourni par la source)

Increase in invasive group A streptococcal infections and emergence of novel, rapidly expanding sub-lineage of the virulent Streptococcus pyogenes M1 clone, Denmark, 2023

Thor Bech Johannesen, Charlotte Munkstrup, Sofie Marie Edslev, Sharmin Jamshid Baig et autres

A highly virulent sub-lineage of the Streptococcus pyogenes M1 clone has been rapidly expanding throughout Denmark since late 2022 and now accounts for 30% of the new invasive group A streptococcal infections. We aimed to investigate whether a shift in variant composition …

dk, is, au (code pays fourni par la source)

Design and validation of Dolosigranulum pigrum specific PCR primers using the bacterial core genome

Maliha Aziz, Amber Palmer, Søren Iversen, Juan E. Salazar et autres

Abstract Dolosigranulum pigrum—a lactic acid bacterium that is increasingly recognized as an important member of the nasal microbiome. Currently, there are limited rapid and low-cost options for confirming D. pigrum isolates and detecting D. pigrum in clinical specimens. Here we describe the …

us, dk, de (code pays fourni par la source)

Dramatic increase in slaughter condemnations due to Escherichia coli ST23 and ST101 within the Danish broiler production

Sofie Kromann, Sharmin Jamshid Baig, Rikke Heidemann Olsen, Sofie Marie Edslev et autres

Escherichia coli constitutes a major challenge to poultry even when the prevalence of colibacillosis is low. Additionally, specific E. coli strains can severely enhance the detrimental effects on productivity, animal welfare and antimicrobial use. In 2019-2020, a dramatic increase in colibacillosis occurred …

dk (code pays fourni par la source)

Longitudinal study on background lesions in broiler breeder flocks and their progeny, and genomic characterisation of Escherichia coli

Sofie Kromann, Sharmin Jamshid Baig, Marc Stegger, Rikke Heidemann Olsen et autres

In broiler breeders, background mortality is rarely addressed, however, it represents the death of a vast number of birds, a constant productivity loss, welfare concerns and it might affect chick quality. The study aimed to unveil lesions leading to mortality in a …

dk (code pays fourni par la source)

Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark

Thomas Yssing Michaelsen, Marc Bennedbæk, Lasse Engbo Christiansen, Mia S. F. Jørgensen et autres

BACKGROUND: In early 2021, the SARS-CoV-2 lineage B.1.1.7 (Alpha variant) became dominant across large parts of the world. In Denmark, comprehensive and real-time test, contact-tracing, and sequencing efforts were applied to sustain epidemic control. Here, we use these data to investigate the …

dk (code pays fourni par la source)

Genome analysis of Legionella pneumophila ST23 from various countries reveals highly similar strains

Maria Luisa Ricci, Silvia Fillo, Andrea Ciammaruconi, Florigio Lista et autres

serogroup 1 (Lp1) sequence type (ST) 23 is one of the most commonly detected STs in Italy where it currently causes all investigated outbreaks. ST23 has caused both epidemic and sporadic cases between 1995 and 2018 and was analysed at genomic level …

it, ch, fr, dk, pt (code pays fourni par la source)