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The overprescribing and misuse of antibiotics have led to the rapid development of multidrug-resistant bacteria, such as those that cause UTIs. UTIs are the most common outpatient infections and are mainly caused by Escherichia coli and Klebsiella spp., although some Gram-positive bacteria, such as Pseudomonas aeruginosa, have been isolated in many cases. The rise of antimicrobial-resistant bacteria is a major public health concern, as it is predicted to lead to increased healthcare costs and poor patient outcomes and is expected to be the leading cause of global mortality by 2050. Antibiotic resistance among bacterial species can arise from a myriad of factors, including intrinsic and acquired resistance mechanisms, as well as mobile genetic elements, such as transposons, integrons, and plasmids. Plasmid-mediated resistance is of major concern as drug-resistance genes can quickly and efficiently spread across bacterial species via horizontal gene transfer. The emergence of extended-spectrum β-lactamases (ESBLs) such as NDM-1, OXA, KPC, and CTX-M family members has conferred resistance to many commonly used antibiotics in the treatment of UTIs, including penicillins, carbapenems, cephalosporins, and sulfamethoxazole. This review will focus on plasmid-mediated bacterial genes, especially those that encode ESBLs, and how they contribute to antibiotic resistance. Early clinical detection of these genes in patient samples will provide better treatment options and reduce the threat of antibiotic resistance. [ABSTRACT FROM AUTHOR]

Quantification of heritability is a fundamental desideratum in genetics, which allows an assessment of the contribution of additive genetic variation to the variability of a trait of interest. The traditional computational approaches for assessing the heritability of a trait have been developed in the field of quantitative genetics. However, the rise of modern population genomics with large sample sizes has led to the development of several new machine learning-based approaches to inferring heritability. In this article, we systematically summarize recent advances in machine learning which can be used to infer heritability. We focus on an application of these methods to bacterial genomes, where heritability plays a key role in understanding phenotypes such as antibiotic resistance and virulence, which are particularly important due to the rising frequency of antimicrobial resistance. By designing a heritability model incorporating realistic patterns of genome-wide linkage disequilibrium for a frequently recombining bacterial pathogen, we test the performance of a wide spectrum of different inference methods, including also GCTA. In addition to the synthetic data benchmark, we present a comparison of the methods for antibiotic resistance traits for multiple bacterial pathogens. Insights from the benchmarking and real data analyses indicate a highly variable performance of the different methods and suggest that heritability inference would likely benefit from tailoring of the methods to the specific genetic architecture of the target organism. Availability and implementation The R codes and data used in the numerical experiments are available at: https://github.com/tienmt/her_MLs. [ABSTRACT FROM AUTHOR]

Background: Serratia ureilytica DW2 is a highly efficient phosphate-solubilizing bacteria isolated from Codonopsis pilosula rhizosphere soil that can promote the growth of C. pilosula; nonetheless, until now, no validated reference genes from the genus Serratia have been reported that can be used for the normalization of quantitative real-time polymerase chain reaction (RT--qPCR) data. Methods: To screen stable reference genes of S. ureilytica DW2, the expression of its eight candidate reference genes (16S rRNA, ftsZ, ftsA, mreB, recA, slyD, thiC, and zipA) under different treatment conditions (pH, temperature, culture time, and salt content) was assayed by RT--qPCR. The expression stability of these genes was analyzed using different algorithms (geNorm, NormFinder, and BestKeeper). To verify the reliability of the data, the expression of the glucose dehydrogenase (gdh) gene under different soluble phosphate levels was quantified using the most stably expressed reference gene. Results: The results showed that the zipA and 16S rRNA genes were the most stable reference genes, and the least stable genes were thiC and recA. The expression of gdh was consistent with the phosphate solubilization ability on plates containing the National Botanical Research Institute phosphate growth medium. Conclusion: Therefore, this study provides a stable and reliable reference gene of Serratia for the accurate quantification of functional gene expression in future studies. [ABSTRACT FROM AUTHOR]

ABSTRACT Enzymes involved in rescuing stalled ribosomes and recycling translation machinery are ubiquitous in bacteria and required for growth. Peptidyl tRNA drop-off is a type of abortive translation that results in the release of a truncated peptide that is still bound to tRNA (peptidyl tRNA) into the cytoplasm. Peptidyl tRNA hydrolase (Pth) recycles the released tRNA by cleaving off the unfinished peptide and is essential in most bacteria. We developed a sequencing-based strategy called copper sulfate-based tRNA sequencing (Cu-tRNAseq) to study the physiological role of Pth in Mycobacterium tuberculosis (Mtb). While most peptidyl tRNA species accumulated in a strain with impaired Pth expression, peptidyl prolyl-tRNA was particularly enriched, suggesting that Pth is required for robust peptidyl prolyl-tRNA turnover. Reducing Pth levels increased Mtb’s susceptibility to tRNA synthetase inhibitors that are in development to treat tuberculosis (TB) and rendered this pathogen highly susceptible to macrolides, drugs that are ordinarily ineffective against Mtb. Collectively, our findings reveal the potency of Cu-tRNAseq for profiling peptidyl tRNAs and suggest that targeting Pth would open new therapeutic approaches for TB. IMPORTANCE Peptidyl tRNA hydrolase (Pth) is an enzyme that cuts unfinished peptides off tRNA that has been prematurely released from a stalled ribosome. Pth is essential in nearly all bacteria, including the pathogen Mycobacterium tuberculosis (Mtb), but it has not been clear why. We have used genetic and novel biochemical approaches to show that when Pth levels decline in Mtb, peptidyl tRNA accumulates to such an extent that usable tRNA pools drop. Thus, Pth is needed to maintain normal tRNA levels, most strikingly for prolyl-tRNAs. Many antibiotics act on protein synthesis and could be affected by altering the availability of tRNA. This is certainly true for tRNA synthetase inhibitors, several of which are drug candidates for tuberculosis. We find that their action is potentiated by Pth depletion. Furthermore, Pth depletion results in hypersensitivity to macrolides, drugs that are not active enough under ordinary circumstances to be useful for tuberculosis.

Background: Streptococcus mutans (S. mutans) is a pivotal cariogenic pathogen contributing to its multiple virulence factors, one of which is synthesizing exopolysaccharides (EPS). VicK, a sensor histidine kinase, plays a major role in regulating genes associated with EPS synthesis and adhesion. Here we first identified an antisense vicK RNA (ASvicK) bound with vicK into double-stranded RNA (dsRNA). Objective: This study aims to investigate the effect and mechanism of ASvicK in the EPS metabolism and cariogenesis of S. mutans. Methods: The phenotypes of biofilm were detected by scanning electron microscopy (SEM), gas chromatography-mass spectrometery (GC-MS), gel permeation chromatography (GPC), transcriptome analysis and Western blot. Co-immunoprecipitation (Co-ip) assay and enzyme activity experiment were adopted to investigate the mechanism of ASvicK regulation. Caries animal models were developed to study the relationship between ASvicK and cariogenicity of S. mutans. Results: Overexpression of ASvicK can inhibit the growth of biofilm, reduce the production of EPS and alter genes and protein related to EPS metabolism. ASvicK can adsorb RNase III to regulate vicK and affect the cariogenicity of S. mutans. Conclusions: ASvicK regulates vicK at the transcriptional and post-transcriptional levels, effectively inhibits EPS synthesis and biofilm formation and reduces its cariogenicity in vivo. [ABSTRACT FROM AUTHOR]

This is a systematic review and meta-analysis that evaluated the prevalence of Escherichia coli antibiotic-resistant genes (ARGs) in animals, humans, and the environment in South Africa. This study followed Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines to search and use literature published between 1 January 2000 to 12 December 2021, on the prevalence of South African E. coli isolates' ARGs. Articles were downloaded from African Journals Online, PubMed, ScienceDirect, Scopus, and Google Scholar search engines. A random effects meta-analysis was used to estimate the antibiotic-resistant genes of E. coli in animals, humans, and the environment. Out of 10764 published articles, only 23 studies met the inclusion criteria. The obtained results indicated that the pooled prevalence estimates (PPE) of E. coli ARGs was 36.3%, 34.4%, 32.9%, and 28.8% for blaTEM-M-1, ampC, tetA, and blaTEM, respectively. Eight ARGs (blaCTX-M, blaCTX-M-1, blaTEM, tetA, tetB, sul1, sulII, and aadA) were detected in humans, animals and the environmental samples. Human E. coli isolate samples harboured 38% of the ARGs. Analyzed data from this study highlights the occurrence of ARGs in E. coli isolates from animals, humans, and environmental samples in South Africa. Therefore, there is a necessity to develop a comprehensive "One Health" strategy to assess antibiotics use in order to understand the causes and dynamics of antibiotic resistance development, as such information will enable the formulation of intervention strategies to stop the spread of ARGs in the future. [ABSTRACT FROM AUTHOR]

Oral streptococci are gram-positive facultative anaerobic bacteria that are normal inhabitants of the human oral cavity and play an important role in maintaining oral microecological balance and pathogenesis. Transposon mutagenesis is an effective genetic manipulation strategy for studying the function of genomic features. In order to study cariogenic related genes and crucial biological element genes of oral Streptococcus, transposon mutagenesis was widely used to identify functional genes. With the advent of next-generation sequencing (NGS) technology and the development of transposon random mutation library construction methods, transposon insertion sequencing (TIS) came into being. Benefiting from high-throughput advances in NGS, TIS was able to evaluate the fitness contribution and essentiality of genetic features in the bacterial genome. The application of transposon mutagenesis, including TIS, to oral streptococci provided a massive amount of valuable detailed linkage data between genetic fitness and genetic backgrounds, further clarify the processes of colonization, virulence, and persistence and provides a more reliable basis for investigating relationships with host ecology and disease status. This review focuses on transposon mutagenesis, including TIS, and its applicability in oral streptococci. [ABSTRACT FROM AUTHOR]

Background: Milk yield and fine composition in sheep depend on the volatile and long-chain fatty acids, microbial proteins, vitamins produced through feedstuff digestion by the rumen microbiota. In cattle, the host genome has been shown to have a low to moderate genetic control on rumen microbiota abundance but a high control on dairy traits with heritabilities higher than 0.30. There is little information on the genetic correlations and quantitative trait loci (QTL) that simultaneously affect rumen microbiota abundance and dairy traits in ruminants, especially in sheep. Thus, our aim was to quantify the effect of the host genetics on rumen bacterial abundance and the genetic correlations between rumen bacterial abundance and several dairy traits, and to identify QTL that are associated with both rumen bacterial abundance and milk traits. Results: Our results in Lacaune sheep show that the heritability of rumen bacterial abundance ranges from 0 to 0.29 and that the heritability of 306 operational taxonomic units (OTU) is significantly different from 0. Of these 306 OTU, 96 that belong mainly to the Prevotellaceae, Lachnospiraceae and Ruminococcaceae bacterial families show strong genetic correlations with milk fatty acids and proteins (absolute values ranging from 0.33 to 0.99). Genome-wide association studies revealed a QTL for alpha-lactalbumin concentration in milk on Ovis aries chromosome (OAR) 11, and six QTL for rumen bacterial abundances i.e., for two OTU belonging to the genera Prevotella (OAR3 and 5), Rikeneleaceae_RC9_gut_group (OAR5), Ruminococcus (OAR5), an unknown genus of order Clostridia UCG-014 (OAR10), and CAG-352 (OAR11). None of these detected regions are simultaneously associated with rumen bacterial abundance and dairy traits, but the bacterial families Prevotellaceae, Lachnospiraceae and F082 show colocalized signals on OAR3, 5, 15 and 26. Conclusions: In Lacaune dairy sheep, rumen microbiota abundance is partially controlled by the host genetics and is poorly genetically linked with milk protein and fatty acid compositions, and three main bacterial families, Prevotellaceae, Lachnospiraceae and F082, show specific associations with OAR3, 5, 15 and 26. [ABSTRACT FROM AUTHOR]

Mycobacteria, including the human pathogen Mycobacterium tuberculosis, grow by inserting new cell wall material at their poles. This process and that of division are asymmetric, producing a phenotypically heterogeneous population of cells that respond non-uniformly to stress (Aldridge et al., 2012; Rego et al., 2017). Surprisingly, deletion of a single gene - lamA - leads to more symmetry, and to a population of cells that is more uniformly killed by antibiotics (Rego et al., 2017). How does LamA create asymmetry? Here, using a combination of quantitative time-lapse imaging, bacterial genetics, and lipid profiling, we find that LamA recruits essential proteins involved in cell wall synthesis to one side of the cell - the old pole. One of these proteins, MSMEG_0317, here renamed PgfA, was of unknown function. We show that PgfA is a periplasmic protein that interacts with MmpL3, an essential transporter that flips mycolic acids in the form of trehalose monomycolate (TMM), across the plasma membrane. PgfA interacts with a TMM analog suggesting a direct role in TMM transport. Yet our data point to a broader function as well, as cells with altered PgfA levels have differences in the abundance of other lipids and are differentially reliant on those lipids for survival. Overexpression of PgfA, but not MmpL3, restores growth at the old poles in cells missing lamA. Together, our results suggest that PgfA is a key determinant of polar growth and cell envelope composition in mycobacteria, and that the LamA-mediated recruitment of this protein to one side of the cell is a required step in the establishment of cellular asymmetry. [ABSTRACT FROM AUTHOR]

Despite dramatic advances in genomics, connecting genotypes to phenotypes is still challenging. Sexual genetics combined with linkage analysis is a powerful solution to this problem but generally unavailable in bacteria. We build upon a strong negative selection system to invent mass allelic exchange (MAE), which enables hybridization of arbitrary (including pathogenic) strains of Escherichia coli. MAE reimplements the natural phenomenon of random cross-overs, enabling classical linkage analysis. We demonstrate the utility of MAE with virulence-related gain-of-function screens, discovering that transfer of a single operon from a uropathogenic strain is sufficient for enabling a commensal E. coli to form large intracellular bacterial collections within bladder epithelial cells. MAE thus enables assaying natural allelic variation in E. coli (and potentially other bacteria), complementing existing loss-of-function genomic techniques. [ABSTRACT FROM AUTHOR]

Xanthomonas citri pv. citri (Xcc), a gram-negative bacterium, is the causal agent of citrus canker, one of the most devastating diseases threatening the citrus industry worldwide. Understanding the diversity and population structure of Xcc is a prerequisite for disease epidemiological monitoring and effective disease management. Recent characterization of the clustered regularly interspaced short palindromic repeats (CRISPR)/cas (CRISPR-associated proteins genes) system with a highly variable repeat number among species provides a new molecular typing method for bacterial genetic analysis. In this study, we performed systematic in silico analyses of 28 Xcc genomes and identified a credible CRISPR/cas in Xcc strains. Further analysis of CRISPR polymorphisms (repeat number and spacer types) in 129 Xcc A strains collected from six provinces in China identified 15 types of CRISPR arrays with 25 spacers. Phylogenetic analysis of Xcc strains based on the CRISPR locus produced a more reliable and accurate typing result compared to the commonly used loci. In addition, seven associated cas genes--cas 1, cas 2, cas 3, cas 4, cas 5, cas 7 (csd 2), and cas 8 (csd 1)--were found located adjacent to the CRISPR array. BLAST results showed > 99% similarity of seven cas genes among Xcc strains. Homology analysis of spacer sequences showed that six spacers had possible phage/prophage origin. The characterization of the CRISPR/cas system among Xcc strains provided an updated strain typing method for Xcc diversity analysis and yielded a panoramic view of CRISPR evolution for further studies of Xcc -phage interactions. [ABSTRACT FROM AUTHOR]

Understanding the inheritance pattern of bacterial wilt (BW) disease tolerance is important to maximize genetic potential in eggplant (Solanum melongena L.). The study was conducted employing populations P1, P2, F1, F2, BC1, and BC2 of the crosses 'Utkal Anushree × Bidhan Suphala,' 'Utkal Anushree × Garia,' and 'Utkal Madhuri × Bidhan Super' to understand genetic control of BW disease tolerance. The inheritance study indicated that tolerance to BW disease was conditioned by a single dominant gene in 3 Tolerant × Susceptible crosses. The nature, and magnitude, of gene action controlling inheritance of bacterial wilt-related traits (days to 1st appearance of BW disease and disease incidence of BW) differed between crosses and traits, mostly conditioned by nonadditive gene action and duplicate epistasis. The disparity between results from the chi-square goodness of fit test and other quantitative methods indicated that the chi-square goodness of fit test alone could be misleading in the study of genetic control of bacterial wilt related traits due to its subjectivity. Complementary epitasis in 2 crosses for days to 1st appearance of BW disease would be helpful in improvement of this trait through backcrossing. Duplicate epistasis controlling BW disease incidence suggested selection of desirable recombinants from the segregating population developed from bi-parental mating. The BW-tolerant plants, with an acceptable fruit weight, can be isolated from segregating generations with involvement of susceptible plants having a higher fruit weight. [ABSTRACT FROM AUTHOR]