The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Fangcang shelter hospitals are a novel public health concept. They were implemented for the first time in China in February, 2020, to tackle the coronavirus disease 2019 (COVID-19) outbreak. The Fangcang shelter hospitals in China were large-scale, temporary hospitals, rapidly built by converting existing public venues, such as stadiums and exhibition centres, into health-care facilities. They served to isolate patients with mild to moderate COVID-19 from their families and communities, while providing medical care, disease monitoring, food, shelter, and social activities. We document the development of Fangcang shelter hospitals during the COVID-19 outbreak in China and explain their three key characteristics (rapid construction, massive scale, and low cost) and five essential functions (isolation, triage, basic medical care, frequent monitoring and rapid referral, and essential living and social engagement). Fangcang shelter hospitals could be powerful components of national responses to the COVID-19 pandemic, as well as future epidemics and public health emergencies.

Fangcang shelter hospitals: a novel concept for responding to public health emergencies

Antibiotic resistance is a major global health challenge and, worryingly, several key Gram negative pathogens can become resistant to most currently available antibiotics. Polymyxins have been revived as a last-line therapeutic option for the treatment of infections caused by multidrug-resistant Gram negative bacteria, in particular Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacterales. Polymyxins were first discovered in the late 1940s but were abandoned soon after their approval in the late 1950s as a result of toxicities (e.g., nephrotoxicity) and the availability of "safer" antibiotics approved at that time. Therefore, knowledge on polymyxins had been scarce until recently, when enormous efforts have been made by several research teams around the world to elucidate the chemical, microbiological, pharmacokinetic/pharmacodynamic, and toxicological properties of polymyxins. One of the major achievements is the development of the first scientifically based dosage regimens for colistin that are crucial to ensure its safe and effective use in patients. Although the guideline has not been developed for polymyxin B, a large clinical trial is currently being conducted to optimize its clinical use. Importantly, several novel, safer polymyxin-like lipopeptides are developed to overcome the nephrotoxicity, poor efficacy against pulmonary infections, and narrow therapeutic windows of the currently used polymyxin B and colistin. This review discusses the latest achievements on polymyxins and highlights the major challenges ahead in optimizing their clinical use and discovering new-generation polymyxins. To save lives from the deadly infections caused by Gram negative "superbugs," every effort must be made to improve the clinical utility of the last-line polymyxins. SIGNIFICANCE STATEMENT: Antimicrobial resistance poses a significant threat to global health. The increasing prevalence of multidrug-resistant (MDR) bacterial infections has been highlighted by leading global health organizations and authorities. Polymyxins are a last-line defense against difficult-to-treat MDR Gram negative pathogens. Unfortunately, the pharmacological information on polymyxins was very limited until recently. This review provides a comprehensive overview on the major achievements and challenges in polymyxin pharmacology and clinical use and how the recent findings have been employed to improve clinical practice worldwide.

https://pharmrev.aspetjournals.org/content/pharmrev/73/2/679.full.pdf

Rescuing the Last-Line Polymyxins: Achievements and Challenges

Antibiotics are life-saving medicines, but many bacteria now have the ability to resist their effects. For some infections, all frontline antibiotics are now ineffective. To treat infections caused by these highly resistant bacteria, clinicians must use so-called ‘antibiotics of last resort’. These antibiotics include a drug called colistin, which is moderately effective, but often fails to eradicate the infection. One of the challenges to making colistin more effective is that its mechanism is poorly understood. Bacteria have two layers of protection against the outside world: an outer cell membrane and an inner cell membrane. To kill them, colistin must punch holes in both. First, it disrupts the outer membrane by interacting with molecules called lipopolysaccharides. But how it disrupts the inner membrane was unclear. Bacteria have evolved several different mechanisms that make them resistant to the effects of colistin. Sabnis et al. reasoned that understanding how these mechanisms protected bacteria could reveal how the antibiotic works to damage the inner cell membrane. Sabnis et al. examined the effects of colistin on Escherichia coli bacteria with and without resistance to the antibiotic. Exposing these bacteria to colistin revealed that the antibiotic damages both layers of the cell surface in the same way, targeting lipopolysaccharide in the inner membrane as well as the outer membrane. Next, Sabnis et al. used this new information to make colistin work better. They found that the effects of colistin were magnified when it was combined with the experimental antibiotic murepavadin, which caused lipopolysaccharide to build up at the inner membrane. This allowed colistin to punch more holes through the inner membrane, making colistin more effective at killing bacteria. To find out whether this combination of colistin and murepavadin could work as a clinical treatment, Sabnis et al. tested it on mice with Pseudomonas aeruginosa infections in their lungs. Colistin was much better at killing Pseudomonas aeruginosa and treating infections when combined with murepavadin than it was on its own. Pseudomonas aeruginosa bacteria can cause infections in the lungs of people with cystic fibrosis. At the moment, patients receive colistin in an inhaled form to treat these infections, but it is not always successful. The second drug used in this study, murepavadin, is about to enter clinical trials as an inhaled treatment for lung infections too. If the trial is successful, it may be possible to use both drugs in combination to treat lung infections in people with cystic fibrosis.

Colistin kills bacteria by targeting lipopolysaccharide in the cytoplasmic membrane.

Potential sources, modes of transmission and effectiveness of prevention measures against SARS-CoV-2.

Mobile colistin resistance (mcr) genes represent an emerging challenge. Here we describe a novel mcr gene, mcr-10, on an IncFIA plasmid of an Enterobacter roggenkampii clinical strain. mcr-10 has t...

https://www.tandfonline.com/doi/pdf/10.1080/22221751.2020.1732231

Identification of novel mobile colistin resistance gene mcr-10

The contamination of patients' surroundings by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains understudied We sampled the surroundings and the air of six negative-pressure non-intensive care unit (non-ICU) rooms in a designated isolation ward in Chengdu, China, that were occupied by 13 laboratory-confirmed coronavirus disease 2019 (COVID-19) patients who had returned from overseas travel, including 2 asymptomatic patients A total of 44 of 112 (393%) surface samples were positive for SARS-CoV-2 as detected by real-time PCR, suggesting extensive contamination, although all of the air samples were negative In particular, in a single room occupied by an asymptomatic patient, four sites were SARS-CoV-2 positive, highlighting that asymptomatic COVID-19 patients do contaminate their surroundings and impose risks for others with close contact Placement of COVID-19 patients in rooms with negative pressure may bring a false feeling of safety, and the importance of rigorous environment cleaning should be emphasizedIMPORTANCE Although it has been well recognized that the virus SARS-CoV-2, the causative agent of COVID-19, can be acquired by exposure to fomites, surprisingly, the contamination of patients' surroundings by SARS-CoV-2 is largely unknown, as there have been few studies We performed an environmental sampling study for 13 laboratory-confirmed COVID-19 patients and found extensive contamination of patients' surroundings In particular, we found that asymptomatic COVID-19 patients contaminated their surroundings and therefore imposed risks for other people Environment cleaning should be emphasized in negative-pressure rooms The findings may be useful to guide infection control practice to protect health care workers

Asymptomatic COVID-19 Patients Can Contaminate Their Surroundings: an Environment Sampling Study.

There is an urgent need to understand the global epidemiological landscape of carbapenem-resistant Escherichia coli (CREC). Here we provide combined genomic and phenotypic characterization of the emergence of a CREC clone from the ST410 lineage. We show that the clone expands with a single plasmid, within which there is frequent switching of the carbapenemase gene type between blaNDM and blaOXA-181 with no impact on plasmid stability or fitness. A search for clone-specific traits identified unique alleles of genes involved in adhesion and iron acquisition, which have been imported via recombination. These recombination-derived allelic switches had no impact on virulence in a simple infection model, but decreased efficiency in binding to abiotic surfaces and greatly enhanced fitness in iron limited conditions. Together our data show a footprint for evolution of a CREC clone, whereby recombination drives new alleles into the clone which provide a competitive advantage in colonizing mammalian hosts. Yu Feng, Lu Liu, Alan McNally et al. provide genomic and phenotypic characterization of a carbapenem-resistant E. coli clone from the ST410 lineage. They show a footprint for the evolution of this clone where recombination-derived new alleles provide competitive advantage in colonizing mammalian hosts.

/pdf/key-evolutionary-events-in-the-emergence-of-a-globally-2gsiif3oyn.pdf

Key evolutionary events in the emergence of a globally disseminated, carbapenem resistant clone in the Escherichia coli ST410 lineage.

A strain of a member of the genus 
Klebsiella
, WCHKl090001, was recovered from a human urine sample in PR China in 2017. Phylogenetic analysis based on gyrA and rpoB housekeeping genes revealed that the strain was distinct from any previously described species of the genus 
Klebsiella
though it was clustered with the Klebsiella oxytoca phylogroup, including 
Klebsiella
grimontii, 
Klebsiella
michiganensis and 
Klebsiella
oxytoca. The whole-genome sequence of strain WCHKl090001 has an up to 87.18 % average nucleotide identity with those of type strains of all known species of the genus 
Klebsiella
. In silico DNA–DNA hybridization (isDDH) values between strain WCHKl090001 and type strains of all known species of the genus Klebsiella ranged from 22.3 to 35.2 %. Strain WCHKl090001 could be distinguished from species of the 
Klebsiella oxytoca
phylogroup by its negative Voges–Proskauer reaction. Genotypic and phenotypic characteristics from this study indicate that strain WCHKl090001 should be considered to represent a novel species of the genus 
Klebsiella
, for which the name 
Klebsiella
huaxiensis sp. nov. is proposed. The type strain is WCHKl090001T (=GDMCC 1.1379T=CNCTC 7650T).

Klebsiella huaxiensis sp. nov., recovered from human urine

Handwashing sinks as the source of transmission of ST16 carbapenem-resistant Klebsiella pneumoniae, an international high-risk clone, in an intensive care unit

Li Wei

Papers

Identification of novel mobile colistin resistance gene mcr-10

Asymptomatic COVID-19 Patients Can Contaminate Their Surroundings: an Environment Sampling Study.

Key evolutionary events in the emergence of a globally disseminated, carbapenem resistant clone in the Escherichia coli ST410 lineage.

Klebsiella huaxiensis sp. nov., recovered from human urine

Handwashing sinks as the source of transmission of ST16 carbapenem-resistant Klebsiella pneumoniae, an international high-risk clone, in an intensive care unit