Monthly Notices is one of the three largest general primary astronomical research publications. It is an international journal, published by the Royal Astronomical Society. This article 1 describes its publication policy and practice.

Monthly Notices of the Royal Astronomical Society

The redshifted 21 cm line is an emerging tool in cosmology, in principle permitting three-dimensional surveys of our Universe that reach unprecedentedly large volumes, previously inaccessible length scales, and hitherto unexplored epochs of our cosmic timeline. Large radio telescopes have been constructed for this purpose, and in recent years there has been considerable progress in transforming 21 cm cosmology from a field of considerable theoretical promise to one of observational reality. Increasingly, practitioners in the field are coming to the realization that the success of observational 21cm cosmology will hinge on software algorithms and analysis pipelines just as much as it does on careful hardware design and telescope construction. This review provides a pedagogical introduction to state-of-the-art ideas in 21 cm data analysis, covering a wide variety of steps in a typical analysis pipeline, from calibration to foreground subtraction to mapmaking to power spectrum estimation to parameter estimation.

Data Analysis for Precision 21 cm Cosmology

We present a detection of 21 cm emission from large-scale structure (LSS) between redshift 0.78 and 1.43 made with the Canadian Hydrogen Intensity Mapping Experiment. Radio observations acquired over 102 nights are used to construct maps that are foreground filtered and stacked on the angular and spectral locations of luminous red galaxies (LRGs), emission-line galaxies (ELGs), and quasars (QSOs) from the eBOSS clustering catalogs. We find decisive evidence for a detection when stacking on all three tracers of LSS, with the logarithm of the Bayes factor equal to 18.9 (LRG), 10.8 (ELG), and 56.3 (QSO). An alternative frequentist interpretation, based on the likelihood ratio test, yields a detection significance of 7.1σ (LRG), 5.7σ (ELG), and 11.1σ (QSO). These are the first 21 cm intensity mapping measurements made with an interferometer. We constrain the effective clustering amplitude of neutral hydrogen (H i), defined as HI≡103ΩHIbHI+〈fμ2〉 , where ΩH i is the cosmic abundance of H i, b H i is the linear bias of H i, and 〈f μ 2〉 = 0.552 encodes the effect of redshift-space distortions at linear order. We find HI=1.51−0.97+3.60 for LRGs (z = 0.84), HI=6.76−3.79+9.04 for ELGs (z = 0.96), and HI=1.68−0.67+1.10 for QSOs (z = 1.20), with constraints limited by modeling uncertainties at nonlinear scales. We are also sensitive to bias in the spectroscopic redshifts of each tracer, and we find a nonzero bias Δ v = − 66 ± 20 km s−1 for the QSOs. We split the QSO catalog into three redshift bins and have a decisive detection in each, with the upper bin at z = 1.30 producing the highest-redshift 21 cm intensity mapping measurement thus far.

Detection of Cosmological 21 cm Emission with the Canadian Hydrogen Intensity Mapping Experiment

Mobile tigecycline resistance (MTR) threatens the clinical efficacy of the salvage antibiotic, tigecycline (TIG) used in treating deadly infections in humans caused by superbugs (multidrug-, extensively drug-, and pandrug-resistant bacteria), including carbapenem- and colistin-resistant bacteria. Currently, non-mobile tet(X) and mobile plasmid-mediated transmissible tet(X) and resistance-nodulation-division (RND) efflux pump tmexCD-toprJ genes, conferring high-level TIG (HLT) resistance have been detected in humans, animals, and environmental ecosystems. Given the increasing rate of development and spread of plasmid-mediated resistance against the two last-resort antibiotics, colistin (COL) and TIG, there is a need to alert the global community on the emergence and spread of plasmid-mediated HLT resistance and the need for nations, especially developing countries, to increase their antimicrobial stewardship. Justifiably, MTR spread projects One Health ramifications and portends a monumental threat to global public and animal health, which could lead to outrageous health and economic impact due to limited options for therapy. To delve more into this very important subject matter, this current work will discuss why MTR is an emerging health catastrophe requiring urgent One Health global intervention, which has been constructed as follows: (a) antimicrobial activity of TIG; (b) mechanism of TIG resistance; (c) distribution, reservoirs, and traits of MTR gene-harboring isolates; (d) causes of MTR development; (e) possible MTR gene transfer mode and One Health implication; and (f) MTR spread and mitigating strategies.

https://www.frontiersin.org/articles/10.3389/fmicb.2022.808744/pdf

Mobile Tigecycline Resistance: An Emerging Health Catastrophe Requiring Urgent One Health Global Intervention

This study aimed to investigate the prevalence and characterization of tet(X4) in Escherichia coli isolates from a pig farm in Shanghai, China, and to elucidate tet(X4) dissemination mechanism in this swine farm. Forty-nine (80.33%) E. coli strains were isolated from 61 samples from a pig farm and were screened for the presence of tet(X). Among them, six (12.24%) strains were positive for tet(X4) and exhibited resistance to tigecycline (MIC ≥ 16 mg/L). They were further sequenced by Illumina Hiseq. Six tet(X4)-positive strains belonged to ST761 with identical resistance genes, resistance profiles, plasmid replicons, and cgMLST type except that additional ColE10 plasmid was present in isolate SH21PTE35. Isolate SH21PTE31, as a representative ST761 E. coli strain, was further sequenced using Nanopore MinION. The tet(X4) in SH21PTE31 was located on IncFIA18/IncFIB(K)/IncX1 hybrid plasmid pYUSHP31-1, highly similar to other tet(X4)-carrying IncFIA18/IncFIB(K)/IncX1 plasmids from ST761 E. coli and other E. coli lineages in China. These IncFIA18/IncFIB(K)/IncX1 plasmids shared closely related multidrug resistance regions, and could reorganize, acquire or lose resistance modules mediated by mobile elements such as ISCR2 and IS26. Phylogenetic analysis were performed including all tet(X4)-positive isolates obtained in this pig farm combined with 43 tet(X4)-positive E. coli from pigs, cow, pork, wastewater, and patients with the same ST from NCBI. The 50 tet(X4)-carrying E. coli ST761 isolates from different areas in China shared a close phylogenetic relationship (0-49 SNPs). In conclusion, clonal transmission of tet(X4)-positive E. coli ST761 has occurred in this swine farm. E. coli ST761 has the potential to become a high-risk clone for tet(X4) dissemination in China.

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Tigecycline-resistant Escherichia coli ST761 carrying tet(X4) in a pig farm, China

The 21~cm intensity mapping experiments promise to measure the baryon acoustic oscillations (BAO) through the mapping of H{\small I} gas at the post-reionization epoch. Its success depends on the assumption that H{\small I} gas traces the matter density distribution {\it linearly} on large scales. However, both nonlinear halo clustering and nonlinear effects modulating H{\small I} gas in halos may spoil this. We employ three approaches to generate the mock H{\small I} density from a large-scale N-body simulation at low redshifts, and demonstrate that the assumption of H{\small I} linearity is valid at the scale corresponding to the first BAO peak, but breaks down at $k \gtrsim 0.1\,h\, {\rm Mpc}^{-1}$. The nonlinear effects of halo clustering and H{\small I} content modulation counteract each other at small scales, and their competition results in a model-dependent "sweet-spot" redshift near $z$=1 where the H{\small I} bias is scale-independent down to small scales. We also find that the linear H{\small I} bias scales approximately linearly with redshift for $z\le 3$.

Can HI gas trace the matter density distribution linearly on large scales

The 21 cm intensity mapping experiments promise to obtain the large-scale distribution of HI gas at the post-reionization epoch. In order to reveal the underlying matter density fluctuations from the HI mapping, it is important to understand how HI gas traces the matter density distribution. Both nonlinear halo clustering and nonlinear effects modulating HI gas in halos may determine the scale below which the HI bias deviates from linearity. We employ three approaches to generate the mock HI density from a large-scale N-body simulation at low redshifts, and demonstrate that the assumption of HI linearity is valid at the scale corresponding to the first peak of baryon acoustic oscillations, but breaks down at $k \gtrsim 0.1\,h\, {\rm Mpc}^{-1}$. The nonlinear effects of halo clustering and HI content modulation counteract each other at small scales, and their competition results in a model-dependent "sweet-spot" redshift near $z$=1 where the HI bias is scale-independent down to small scales. We also find that the linear HI bias scales approximately linearly with redshift for $z\le 3$.

The Breakdown Scale of HI Bias Linearity.

• Co-resistance to carbapenem and tigecycline was observed in Klebsiella pneumoniae ST617. • The bla KPC-2 gene was located in a conjugative plasmids associated with a commonly observed core structure. • The tet (A) variant may account for tigecycline resistance. 

Emergence of carbapenem- and tigecycline-resistant Klebsiella pneumoniae ST617.

Colistin is a last-resort antibiotic for severe infections caused by multidrug-resistant (MDR) Gram-negative pathogens. Colistin resistance genes mcr, particularly mcr-1, have been found in Enterobacteriaceae around the world, mainly in Escherichia coli and Salmonella. Salmonella enterica is a major foodborne pathogen, with MDR Salmonella being considered a “Serious Threat Level pathogen” by the Centers for Disease Control and Prevention. ABSTRACT This study aimed to investigate the prevalence and genomic characteristics of the colistin resistance gene mcr in Salmonella enterica in China. In total, 445 S. enterica isolates from animals and food products were screened through PCR and sequencing for the presence of mcr. The mcr genes were detected in nine Salmonella strains (2.02%), with complete mcr-1 in S. enterica serovar Indiana (n = 1) and an S. Typhimurium monophasic variant (S. 4,[5],12:i:-; n = 1), mcr-4.3 in S. enterica serovar London (n = 1), and an incomplete mcr-1 in S. Indiana (n = 6). They exhibited MIC values of 0.25 to 8 mg/L to colistin and showed resistance to multiple antimicrobial agents. Whole-genome sequencing was performed on mcr-positive Salmonella strains using Illumina HiSeq or PacBio single-molecule real-time sequencing. The complete mcr-1 gene was located on conjugative IncN1-IncHI2 plasmid and IncX4 plasmid, respectively, with high similarity to other mcr-1-bearing plasmids belonging to the same incompatibility type. Together with an additional 13 antimicrobial resistance genes, the incomplete mcr-1 was embedded in an 81,442-bp multiresistance region on the chromosome in S. Indiana YZ20MCS6. The Δmcr-1-pap2 segment and a set of tellurite resistance determinants (terYXWZABCDEF) in six S. Indiana strains were similar to other IncHI2 plasmid backbones. The mcr-4.3 gene was located on an untyped plasmid pYULZMPS10. Although low prevalence of mcr was observed in Salmonella, continuous surveillance of this gene in Salmonella is required. Plasmids play an important role in mcr transmission, and mcr-1, although incomplete, can be captured by chromosomes with the help of mobile elements. IMPORTANCE Colistin is a last-resort antibiotic for severe infections caused by multidrug-resistant (MDR) Gram-negative pathogens. Colistin resistance genes mcr, particularly mcr-1, have been found in Enterobacteriaceae around the world, mainly in Escherichia coli and Salmonella. Salmonella enterica is a major foodborne pathogen, with MDR Salmonella being considered a “Serious Threat Level pathogen” by the Centers for Disease Control and Prevention. Therefore, the prevalence of mcr in Salmonella strains must be monitored. In this study, a low mcr prevalence (2.02%) was observed in Salmonella strains from animals and food products, with plasmid-borne mcr-1 in S. enterica serovar Indiana and an S. Typhimurium monophasic variant (S. 4,[5],12:i:-) and chromosomally located mcr-1 in S. Indiana. The mcr-4.3 gene was first identified in S. enterica serovar London associated with an untyped plasmid. Although this study reports a low mcr prevalence in Salmonella, the transmission ability of mcr-positive Salmonella strains to humans via the food chain is a public health concern.

Zhenyuan Wang

Papers

Tigecycline-resistant Escherichia coli ST761 carrying tet(X4) in a pig farm, China

Can HI gas trace the matter density distribution linearly on large scales

The Breakdown Scale of HI Bias Linearity.

Emergence of carbapenem- and tigecycline-resistant Klebsiella pneumoniae ST617.

Chromosomally and Plasmid-Located mcr in Salmonella from Animals and Food Products in China