Advanced Molecular Detection Clips Content (Published on 12/02/2021)
NEWS
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An AI Finds Superbug-Killing Potential in Human Proteins
Levy MG. Wired, Nov 30, 2021. -
The Coronavirus in a Tiny Drop
Zimmer C, Corum J. New York Times, Dec 1, 2021. -
To catch variants like omicron, the world needs to sequence way more virus genes
Irfan U. Vox, Dec 1, 2021. -
Where did 'weird' Omicron come from?
Kupferschmidt K. Science, Dec 1, 2021. -
How 2 Flights to Europe May Have Spurred Spread of New Variant
Horowitz J. New York Times, Nov 30, 2021. -
Omicron COVID variant was in Europe before South African scientists detected and flagged it to the world
CBS, Nov 30, 2021. -
US tracking of virus variants has improved after slow start
Johnson CK. AP, Nov 30, 2021. -
Heavily mutated coronavirus variant puts scientists on alert
Callaway E. Nature, Nov 25, 2021. -
Some experts suggest Omicron variant may have evolved in an animal host
Branswell H. STAT, Dec 2, 2021. -
Do vaccines protect against long COVID? What the data say
Ledford H. Nature, Nov 23, 2021. -
COVID-19 Vaccine Makers Plan for Annual Boosters, but It's Not Clear They'll Be Needed
Rubin R. JAMA, Nov 24, 2021.
EVENTS / TRAINING / WEB RESOURCES
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Train-the-Trainer as an Effective Approach to Building Global Networks of Experts in Genomic Surveillance of Antimicrobial Resistance (AMR).
Abrudan Monica et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 12 (Supplement_4) S283-S289
POLICY
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Africa Centres for Disease Control and Prevention's Statement regarding the new SARS-COV-2 virus variant B.1.1.529
Africa CDC, Nov 26, 2021. -
Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern
WHO, Nov 26, 2021.
CONCEPTS / COMMENTS
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Using a One Health approach to prioritize zoonotic diseases in China, 2019.
Wang Xin et al. PloS one 2021 11 (11) e0259706 -
Is the Medium Still the Message? Culture-Independent Diagnosis of Gastrointestinal Infections.
Sood Neil et al. Digestive diseases and sciences 2021 11 -
Implementing Whole-Genome Sequencing for Ongoing Surveillance of Antimicrobial Resistance: Exemplifying Insights Into Klebsiella pneumoniae.
Aanensen David M et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 12 (Supplement_4) S255-S257 -
CRISPR inactivation by integration
Bondy-Denomy J. Nat Microbiol, Nov 24, 2021. -
Africa: tackle HIV and COVID-19 together
Msomi N, et al. Nature, Dec 1, 2021. -
Peering into Avian Influenza A(H5N8) for a Framework towards Pandemic Preparedness.
Yeo Joshua Yi et al. Viruses 2021 11 (11)
METHODS / TOOLS
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The clinical utility of two high-throughput 16S rRNA gene sequencing workflows for taxonomic assignment of unidentifiable bacterial pathogens in MALDI-TOF MS.
Lao Hiu-Yin et al. Journal of clinical microbiology 2021 11 JCM0176921 -
RFPlasmid: predicting plasmid sequences from short-read assembly data using machine learning.
van der Graaf-van Bloois Linda et al. Microbial genomics 2021 11 (11) -
Overcoming Data Bottlenecks in Genomic Pathogen Surveillance.
Afolayan Ayorinde O et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 12 (Supplement_4) S267-S274 -
Integrating Scalable Genome Sequencing Into Microbiology Laboratories for Routine Antimicrobial Resistance Surveillance.
Kekre Mihir et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 12 (Supplement_4) S258-S266 -
Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Mycobacterium tuberculosis.
Peker Nilay et al. Microbial genomics 2021 11 (11) -
Identification of isolated or mixed strains from long reads: a challenge met on Streptococcus thermophilus using a MinION sequencer.
Siekaniec Grégoire et al. Microbial genomics 2021 11 (11) -
Comprehensive and accurate genetic variant identification from contaminated and low-coverage Mycobacterium tuberculosis whole genome sequencing data.
Heupink Tim H et al. Microbial genomics 2021 11 (11) -
Culture-Independent Detection of Poliovirus in Stool Samples by Direct RNA Extraction.
Harrington Chelsea et al. Microbiology spectrum 2021 11 e0066821
EVOLUTION / ECOLOGY / POPULATIONS
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Phylogenetic Analysis Reveals Source Attribution Patterns for Campylobacter spp. in Tennessee and Pennsylvania.
Lauren K Hudson et al. Microorganisms 2021 11 (11) -
Molecular epidemiology and phylogenomic analysis of Mycobacterium abscessus clinical isolates in an Asian population.
Chew Ka Lip et al. Microbial genomics 2021 11 (11) -
Genome evolution drives transcriptomic and phenotypic adaptation in Pseudomonas aeruginosa during 20 years of infection.
Wardell Samuel J T et al. Microbial genomics 2021 11 (11) -
Emergence and global spread of Listeria monocytogenes main clinical clonal complex.
Moura Alexandra et al. Science advances 2021 12 (49) eabj9805 -
Biogeography and genetic diversity of clinical isolates of Burkholderia pseudomallei in Sri Lanka.
Jayasinghearachchi Himali S et al. PLoS neglected tropical diseases 2021 12 (12) e0009917 -
Extensive Genome Exploration of Clostridium botulinum Group III Field Strains.
Fillo Silvia et al. Microorganisms 2021 11 (11) -
Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis.
Beale Mathew A et al. Nature microbiology 2021 11 (12) 1549-1560 -
Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021.
Bui Ngoc-Niem et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 12 105164 -
Emergence of SARS-CoV-2 Delta Variant, Benin, May-July 2021.
Yadouleton Anges et al. Emerging infectious diseases 2021 11 (1) -
Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak.
Limaye Sanket et al. Viruses 2021 11 (11) -
Genetic Analysis of SARS-CoV-2 Variants in Mexico during the First Year of the COVID-19 Pandemic.
Taboada Blanca et al. Viruses 2021 11 (11) -
Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms.
Barona-Gómez Francisco et al. Microbial genomics 2021 11 (11) -
SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021.
Sarwar Muhammad Bilal et al. Microbial genomics 2021 11 (11) -
Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak.
Oliveira Mauro M et al. Virology journal 2021 11 (1) 222 -
The Dominance of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 and Its Sublineages and Associations with Mortality during the COVID-19 Pandemic in India between 2020 and 2021.
Venkatraja Bakilapadvu et al. The American journal of tropical medicine and hygiene 2021 11 -
Determining international spread of novel B.1.1.523 SARS-CoV-2 lineage
Zemaitis L, et al. medRxiv, Nov 24, 2021. -
SARS-CoV-2 within-host and in-vitro genomic variability and sub-genomic RNA levels indicate differences in viral expression between clinical and in-vitro cohorts.
Johnson-Mackinnon JC, et al. medRxiv, Nov 24, 2021. -
A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain).
Andrés Cristina et al. Emerging microbes & infections 2021 11 1-30 -
Exploring the Diversity of the Human Blood Virome.
Cebriá-Mendoza María et al. Viruses 2021 11 (11) -
Genetic Characterization of Novel H7Nx Low Pathogenic Avian Influenza Viruses from Wild Birds in South Korea during the Winter of 2020-2021.
Lee Yu-Na et al. Viruses 2021 11 (11) -
Emergence of a novel recombinant of CV-A5 in HFMD epidemics in Xiangyang, China.
Yu Yuting et al. BMC medical genomics 2021 11 (1) 279 -
Characterization of Swine Influenza A(H1N2) Variant, Alberta, Canada, 2020.
Kanji Jamil N et al. Emerging infectious diseases 2021 11 (12) 3045-3051 -
Ecology, evolution and spillover of coronaviruses from bats.
Ruiz-Aravena Manuel et al. Nature reviews. Microbiology 2021 11 -
Molecular epidemiology of Paracoccidiodes spp. recovered from patients with paracoccidioidomycosis in a teaching hospital from Minas Gerais State of Brazil.
Andrade-Silva Juliana et al. PLoS neglected tropical diseases 2021 11 (11) e0009956
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Antimicrobial resistance determinants are associated with Staphylococcus aureus bacteraemia and adaptation to the healthcare environment: a bacterial genome-wide association study.
Young Bernadette C et al. Microbial genomics 2021 11 (11) -
A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile.
Imwattana Korakrit et al. Microbial genomics 2021 11 (11) -
Anatomy of an extensively drug-resistant Klebsiella pneumoniae outbreak in Tuscany, Italy.
Martin Melissa J et al. Proceedings of the National Academy of Sciences of the United States of America 2021 11 (48) -
Next-generation sequencing to characterize pyrazinamide resistance in Mycobacterium tuberculosis isolates from two Balkan countries.
Sodja Eva et al. Journal of global antimicrobial resistance 2021 11 -
Plasmodium falciparum pfhrp2 and pfhrp3 gene deletions among patients in the DRC enrolled from 2017 to 2018.
McCaffery Jessica N et al. Scientific reports 2021 11 (1) 22979 -
Characterization of Clinical Escherichia coli Strains Producing a Novel Shiga Toxin 2 Subtype in Sweden and Denmark.
Bai Xiangning et al. Microorganisms 2021 11 (11) -
Quantification of plasmid copy number as surrogate marker of virulence among different invasive and non-invasive genotypes of Chlamydia trachomatis
Lopez-Pintor JM, et al. Diagn Microbiol Infect Dis, Nov 28, 2021. -
Strong Increase in Moxifloxacin Resistance Rate among Multidrug-Resistant Mycobacterium tuberculosis Isolates in China, 2007 to 2013.
Xia Hui et al. Microbiology spectrum 2021 12 e0040921 -
Complexity of Genomic Epidemiology of Carbapenem-Resistant Klebsiella pneumoniae Isolates in Colombia Urges the Reinforcement of Whole Genome Sequencing-Based Surveillance Programs.
Saavedra Sandra Yamile et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 12 (Supplement_4) S290-S299 -
Phenotypic and Molecular Characterization of Commensal, Community-Acquired and Nosocomial Klebsiella spp.
Gómez Marta et al. Microorganisms 2021 11 (11) -
Evaluation of urethrotropic clade meningococcal infection by urine metagenomic shotgun sequencing.
Retchless Adam C et al. Journal of clinical microbiology 2021 11 JCM0173221 -
The N501Y spike substitution enhances SARS-CoV-2 infection and transmission.
Liu Yang et al. Nature 2021 11 -
Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection.
Barber Amelia E et al. Nature microbiology 2021 11 (12) 1526-1536 -
Collateral consequences of agricultural fungicides on pathogenic yeasts: a One Health perspective to tackle azole resistance.
Castelo-Branco Débora et al. Mycoses 2021 11
DETECTION / DIAGNOSIS
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Whole Genome Sequencing Surveillance and Machine Learning of the Electronic Health Record for Enhanced Healthcare Outbreak Detection.
Sundermann Alexander J et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 11 -
Whole Genome Sequencing in the Management of Non-Tuberculous Mycobacterial Infections.
Dohál Matúš et al. Microorganisms 2021 11 (11) -
Rapid Response to SARS-CoV-2 in Aotearoa New Zealand: Implementation of a Diagnostic Test and Characterization of the First COVID-19 Cases in the South Island.
Lawley Blair et al. Viruses 2021 11 (11) -
SARS-CoV-2 and other pathogens in municipal wastewater, landfill leachate, and solid waste: A review about virus surveillance, infectivity, and inactivation.
Anand Uttpal et al. Environmental research 2021 8 111839 -
Looking for a needle in a haystack. SARS-CoV-2 variant characterization in sewage.
Itarte Marta et al. Current opinion in environmental science & health 2021 12 100308 -
Sequencing of SARS-CoV-2 in local transmission cases through Oxford Nanopore MinION platform from Karachi Pakistan.
Mukry Samina Naz et al. Journal of infection in developing countries 2021 11 (10) 1376-1383 -
Show us the Data: Global COVID-19 Wastewater Monitoring Efforts, Equity, and Gaps
Naughton CC, et al. medRxiv, Nov 28, 2021. -
Comparison of residential dormitory COVID-19 monitoring via weekly saliva testing and sewage monitoring.
Fahrenfeld N L et al. The Science of the total environment 2021 11 151947 -
Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR.
Gomes Laksiri et al. Journal of virological methods 2021 11 114374 -
Monitoring SARS-CoV-2 in sewage: Toward sentinels with analytical accuracy.
Calderón-Franco David et al. The Science of the total environment 2021 11 150244 -
Detection of Cytomegalovirus in Urine Dried on Filter Paper.
Minal M Amin et al. J Pediatric Infect Dis Soc 2021 8 (10) 958-961 -
Using Background Sequencing Data to Anticipate DENV-1 Circulation in the Lao PDR.
Calvez Elodie et al. Microorganisms 2021 11 (11) -
Evaluating the Jaccard Similarity Index as a Persistence Measure of Multiple Anal Human Papillomavirus among Nigerian Men Who Have Sex with Men.
Nowak Rebecca G et al. Sexually transmitted diseases 2021 11 -
Missed Plasmodium falciparum and Plasmodium vivax Mixed Infections in Ethiopia Threaten Malaria Elimination.
Leonard Colleen M et al. The American journal of tropical medicine and hygiene 2021 11 -
Immediate pools of malaria infections at diagnosis combined with targeted deep sequencing accurately quantifies frequency of drug resistance mutations.
Aydemir Ozkan et al. PeerJ 2021 11 e11794
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Genomic Investigation and Successful Containment of an Intermittent Common Source Outbreak of OXA-48-Producing Enterobacter cloacae Related to Hospital Shower Drains.
Nurjadi Dennis et al. Microbiology spectrum 2021 11 e0138021 -
Inferring Mycobacterium bovis transmission between cattle and badgers using isolates from the Randomised Badger Culling Trial.
van Tonder Andries J et al. PLoS pathogens 2021 11 (11) e1010075 -
Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines.
Carlos Celia C et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 12 (Supplement_4) S316-S324 -
Genomic investigation of a suspected Klebsiella pneumoniae outbreak in a neonatal care unit in sub-Saharan Africa.
Cornick Jennifer et al. Microbial genomics 2021 11 (11) -
A hospital-wide outbreak of IMI-17-producing Enterobacter ludwigii in an Israeli hospital.
Schechner Vered et al. Antimicrobial resistance and infection control 2021 11 (1) 166 -
Growth, reproduction numbers and factors affecting the spread of SARS-CoV-2 novel variants of concern in the UK from October 2020 to July 2021: a modelling analysis.
Ward Thomas et al. BMJ open 2021 11 (11) e056636 -
COVID-19 in a remote First Nations community in British Columbia, Canada: an outbreak report.
Smith Courtney R et al. CMAJ open 2021 12 (4) E1073-E1079 -
Laboratory analysis of two Delta SARS-CoV-2 variant outbreaks in the Port of Antwerp.
Boogaerts Hélène L F et al. Acta clinica Belgica 2021 12 1-8 -
Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands.
Lu Lu et al. Nature communications 2021 11 (1) 6802 -
SARS-CoV-2 Genomic Surveillance Reveals Little Spread From a Large University Campus to the Surrounding Community.
Valesano Andrew L et al. Open forum infectious diseases 2021 11 (11) ofab518 -
Systematic Genomic and Clinical Analysis of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfections and Recurrences Involving the Same Strain.
Rodríguez-Grande Cristina et al. Emerging infectious diseases 2021 11 (1) -
Genetic epidemiology using whole genome sequencing and haplotype networks revealed the linkage of SARS-CoV-2 infection in nosocomial outbreak.
Ishikawa Fumihiro et al. Infection prevention in practice 2021 11 100190
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Advances in mRNA and other vaccines against MERS-CoV.
Tai Wanbo et al. Translational research : the journal of laboratory and clinical medicine 2021 11 -
Investigating SARS-CoV-2 breakthrough infections per variant and vaccine type
Dingemans J, et al. medRxiv, Nov 24, 2021. -
Increased risk of infection with SARS-CoV-2 Beta, Gamma, and Delta variant compared to Alpha variant in vaccinated individuals
Andeweg SP, et al. medRxiv, Nov 24, 2021. -
Comparative Effectiveness of BNT162b2 and mRNA-1273 Vaccines in U.S. Veterans
Dickerman BA, et al. New Engl J Med, Dec 1, 2021. -
Efficacy and safety of the CVnCoV SARS-CoV-2 mRNA vaccine candidate in ten countries in Europe and Latin America (HERALD): a randomised, observer-blinded, placebo-controlled, phase 2b/3 trial.
Kremsner Peter G et al. The Lancet. Infectious diseases 2021 11
HOST-MICROBE INTERACTIONS
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A genome-wide association study of COVID-19 related hospitalization in Spain reveals genetic disparities among sexes
Spanish COalition to Unlock Research on host GEnetics on COVID-19 (SCOURGE), Carracedo A. medRxiv, Nov 24, 2021. -
Mechanisms of viral inflammation and disease in humans.
Casanova Jean-Laurent et al. Science (New York, N.Y.) 2021 11 (6571) 1080-1086 -
Genetic ancestry effects on the response to viral infection are pervasive but cell type specific.
Randolph Haley E et al. Science (New York, N.Y.) 2021 11 (6571) 1127-1133 -
Is prenatal diet associated with the composition of the vaginal microbiome?
Rosen Emma M et al. Paediatric and perinatal epidemiology 2021 11 -
Effects of Resistant Starch on Symptoms, Fecal Markers and Gut Microbiota in Parkinson's Disease - the RESISTA-PD Trial.
Becker Anouck et al. Genomics, proteomics & bioinformatics 2021 11 -
Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates.
Tuan Vo Phuoc et al. Microbial genomics 2021 11 (11)
Disclaimer: Articles listed in the Advanced Molecular Detection Clips are selected by Public Health Genomics Branch to provide current awareness of the scientific literature and news. Inclusion in the clips does not necessarily represent the views of the Centers for Disease Control and Prevention nor does it imply endorsement of the article's methods or findings. CDC and DHHS assume no responsibility for the factual accuracy of the items presented. The selection, omission, or content of items does not imply any endorsement or other position taken by CDC or DHHS. Opinion, findings and conclusions expressed by the original authors of items included in the Clips, or persons quoted therein, are strictly their own and are in no way meant to represent the opinion or views of CDC or DHHS. References to publications, news sources, and non-CDC Websites are provided solely for informational purposes and do not imply endorsement by CDC or DHHS.
- Page last reviewed:Feb 1, 2024
- Page last updated:Jan 9, 2025