Resistance induction based on the understanding of molecular interactions between plant viruses and host plants

Background Viral diseases cause significant damage to crop yield and quality. While fungi- and bacteria-induced diseases can be controlled by pesticides, no effective approaches are available to control viruses with chemicals as they use the cellular functions of their host for their infection cycle. The conventional method of viral disease control is to use the inherent resistance of plants through breeding. However, the genetic sources of viral resistance are often limited. Recently, genome editing technology enabled the publication of multiple attempts to artificially induce new resistance types by manipulating host factors necessary for viral infection. Main body In this review, we first outline the two major (R gene-mediated and RNA silencing) viral resistance mechanisms in plants. We also explain the phenomenon of mutations of host factors to function as recessive resistance genes, taking the eIF4E genes as examples. We then focus on a new type of virus resistance that has been repeatedly reported recently due to the widespread use of genome editing technology in plants, facilitating the specific knockdown of host factors. Here, we show that (1) an in-frame mutation of host factors necessary to confer viral resistance, sometimes resulting in resistance to different viruses and that (2) certain host factors exhibit antiviral resistance and viral-supporting (proviral) properties. Conclusion A detailed understanding of the host factor functions would enable the development of strategies for the induction of a new type of viral resistance, taking into account the provision of a broad resistance spectrum and the suppression of the appearance of resistance-breaking strains.

Antimicrobial resistance spectrum conferred by pRErm46 of emerging macrolide (multidrug)-resistant Rhodococcus equi

Clonal multidrug resistance recently emerged in Rhodococcus equi , complicating the therapeutic management of this difficult-to-treat animal and human pathogenic actinomycete. The currently spreading multidrug-resistant (MDR) “2287” clone arose in equine farms upon acquisition, and co-selection by mass macrolide-rifampin therapy, of the pRErm46 plasmid carrying the erm (46) macrolides-lincosamides-streptogramins resistance determinant, and an rpoB S531F mutation. Here, we screened a collection of susceptible and macrolide-rifampin-resistant R. equi from equine clinical cases using a panel of 15 antimicrobials against rapidly growing mycobacteria (RGM), nocardiae and other aerobic actinomycetes (NAA). R. equi –including MDR isolates– was generally susceptible to linezolid, minocycline, tigecycline, amikacin and tobramycin according to Staphylococcus aureus interpretive criteria, plus imipenem, cefoxitin and ceftriaxone based on Clinical & Laboratory Standards Institute (CLSI) guidelines for RGM/NAA. Ciprofloxacin and moxifloxacin were in the borderline category according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. Molecular analyses linked pRErm46 to significantly increased MICs for trimethoprim-sulfamethoxazole and doxycycline in addition to clarithromycin within the RGM/NAA panel, and to streptomycin, spectinomycin and tetracycline resistance. pRErm46 variants with spontaneous deletions in the class 1 integron (C1I) region, observed in ≈30% of erm (46)-positive isolates, indicated that the newly identified resistances were attributable to C1I’s sulfonamide ( sul1 ) and aminoglycoside ( aaA9 ) resistance cassettes and adjacent tetRA (33) determinant. Most MDR isolates carried the rpoB S531F mutation of the 2287 clone, while different rpoB mutations (S531L, S531Y) detected in two cases suggest the emergence of novel MDR R. equi strains.

Spectrum of Imipenem and Meropenem Susceptibilities amongst Gram Negative Rods

Aim: To compare the resistance amongst Gram negative bacteria against imipenem and meropenem. Study Design: Prospective, non-randomized, descriptive study. Place and Duration of Study: Department of Microbiology, Mughal Laboratories, Lahore from 1stJuly 2019 to 31stDecember 2019. Methodology: One hundred culture samples received, bacteria isolated and their susceptibilities to imipenem and meropenem were compared. Organisms were recognized by the microbiological techniques according to the current standards and susceptibility testing was done according to the guidelines of Clinical and Laboratory Standards Institute (CLSI) 2020by using Kirby Bauer Disc diffusion method. Results: Salmonella typhi, Citrobacter species and Proteus species were 100% sensitive to imipenem. The rest of bacterial isolates had sensitivities to E. coli 88%, Acinetobacter 80%, Klebsiella species 67% and Peudomonas species 64%. The meropenem is highly resistant in all the bacteria as compared to imipenem. Conclusion: Increasing the trend of carbapenem resistance amongst Gram negative bacteria excluding Salmonella typhi was recorded. Key words: Gram negative rods, Resistance, Spectrum

Heavy Metal-Resistant Filamentous Fungi as Potential Mercury Bioremediators

Filamentous fungi native to heavy metals (HMs) contaminated sites have great potential for bioremediation, yet are still often underexploited. This research aimed to assess the HMs resistance and Hg remediation capacity of fungi isolated from the rhizosphere of plants resident on highly Hg-contaminated substrate. Analysis of Hg, Pb, Cu, Zn, and Cd concentrations by X-ray spectrometry generated the ecological risk of the rhizosphere soil. A total of 32 HM-resistant fungal isolates were molecularly identified. Their resistance spectrum for the investigated elements was characterized by tolerance indices (TIs) and minimum inhibitory concentrations (MICs). Clustering analysis of TIs was coupled with isolates’ phylogeny to evaluate HMs resistance patterns. The bioremediation potential of five isolates’ live biomasses, in 100 mg/L Hg2+ aqueous solution over 48 h at 120 r/min, was quantified by atomic absorption spectrometry. New species or genera that were previously unrelated to Hg-contaminated substrates were identified. Ascomycota representatives were common, diverse, and exhibited varied HMs resistance spectra, especially towards the elements with ecological risk, in contrast to Mucoromycota-recovered isolates. HMs resistance patterns were similar within phylogenetically related clades, although isolate specific resistance occurred. Cladosporium sp., Didymella glomerata, Fusarium oxysporum, Phoma costaricensis, and Sarocladium kiliense isolates displayed very high MIC (mg/L) for Hg (140–200), in addition to Pb (1568), Cu (381), Zn (2092–2353), or Cd (337). The Hg biosorption capacity of these highly Hg-resistant species ranged from 33.8 to 54.9 mg/g dry weight, with a removal capacity from 47% to 97%. Thus, the fungi identified herein showed great potential as bioremediators for highly Hg-contaminated aqueous substrates.

Nontuberculous mycobacteria in China: incidence and antimicrobial resistance spectrum from a nationwide survey

Background Information on the prevalence and resistance spectrum of nontuberculous mycobacteria (NTM) in China is mainly based on regional or local data. To estimate the proportion of NTM cases in China, a national survey of NTM pulmonary disease was carried out based on acid-fast positive sputum samples collected in 2013. Methods Sputum samples collected from enrolled presumptive cases in 72 nationwide tuberculosis surveillance sites from the 31 provinces in the mainland of China were cultured using L-J medium at the National tuberculosis reference laboratory (NTRL). MALDI-TOF MS identified the species of re-cultured strains, and minimal inhibitory concentrations (MICs) were determined to evaluate the drug susceptibility of NTM isolates. Data analysis used statistical software SPSS version 22.0 for Windows statistical package. Results Of 4917 mycobacterial isolates cultured, 6.4% [317/4917, 95% confidence interval (CI) 5.8%–7.2%] were confirmed as NTM, among which 7.7% (287/3709, 95% CI 6.9%–8.6%) were from the southern region. In inland and coastal China, 87.7% (95% CI 78.7%–93.2%) and 50.0% (95% CI 43.7%–56.3%) of isolates, respectively, were slow-growing mycobacteria (SGM), with the remaining rapid growing mycobacteria (RGM). A total of 29 species were detected, Mycobacterium abscessus had higher clarithromycin-inducible resistance rates than M. massiliense (65.67% vs 2.22%). M. kansasii presented lower resistance rates in linezolid and moxifloxacin than M. avium-intracellulare complex (3.23% vs 66.67%, 0 vs 47.22%) and other SGM (3.23% vs 38%, 0 vs 26%). Conclusions More NTM pulmonary disease was observed in the south and coastal China (P < 0.01). SGM was widely distributed, and more RGM are present in southern and coastal China (P < 0.01). The antimicrobial resistance spectrum of different NTM species was significantly different and accurate species identification would be facilitated to NTM pulmonary disease treatment.

Engineering Laboratory/Factory-Specific Phage-Resistant Strains Of Escherichia Coli By Mutagenesis And Selection

Objective: The phage contamination is always a serious problem during operation of Escherichia coli (E. coli). The present study aims to engineer laboratory/factory phage-resistant strains of E. coli based on mutagenesis and selection.Results: The laboratory or factory derived phage was added into a tube containing mutagenized E. coli, resulted in achieving respective phage-resistant E. coli strain. Interestingly, the resistance spectrum of generated phage-resistant strains was not limited to the phage they encountered, which may make these E. coli mutants more resistant to phage contamination. When operation of a resistant strain at the position where the corresponding phage derived from, the phage contamination was completely prevented. There was no significant difference in heterogeneous protein production between the parental strain and the phage-resistant strains. Importantly, the whole process of mutagenesis and selection only required one day.Conclusions: This practical method for engineering laboratory/factory-specific phage-resistant strains may have great potential in resuming E. coli operation in laboratory and factory when the phage contamination outbreaks.

Characteristics of Salmonella From Chinese Native Chicken Breeds Fed on Conventional or Antibiotic-Free Diets

Salmonella is a common food-borne Gram-negative pathogen with multiple serotypes. Pullorum disease, caused by Salmonella Pullorum, seriously threatens the poultry industry. Many previous studies were focused on the epidemiological characteristics of Salmonella infections in conventional antibiotic use poultry. However, little is known about Salmonella infections in chicken flocks fed on antibiotic-free diets. Herein, we investigated and compared Salmonella infections in three Chinese native breeders fed on antibiotic-free diets, including the Luhua, Langya, and Qingjiaoma chickens, and one conventional breeder, the Bairi chicken, via analyzing 360 dead embryos in 2019. The results showed that the main Salmonella serotypes detected in a total of 155 isolates were S. Pullorum (82.6%) and S. Enteritidis (17.4%). Coinfection with two serotypes of Salmonella was specifically found in Bairi chicken. The sequence type (ST) in S. Pullorum was ST92 (n = 96) and ST2151 (n = 32), whereas only ST11 (n = 27) was found in S. Enteritidis. The Salmonella isolates from three breeder flocks fed on antibiotic-free diets exhibited phenotypic heterogeneity with a great variety of drug resistance spectrum. Most of the isolates among three chicken breeds Luhua (64.9%, 50/77), Langya (60%, 12/20) and Qingjiaoma (58.3%, 7/12) fed on antibiotic-free diets were resistant to only one antibiotic (erythromycin), whereas the rate of resistance to one antibiotic in conventional Bairi chicken isolates was only 4.3% (2/46). The multidrug-resistance rate in Salmonella isolates from layer flocks fed on antibiotic-free diets (20.2%, 22/109) was significantly (P &lt; 0.0001) lower than that from chickens fed on conventional diets (93.5%, 43/46). However, high rate of resistance to erythromycin (97.4%~100%) and streptomycin (26%~41.7%) were also found among three breeder flocks fed on antibiotic-free diets, indicating resistance to these antibiotics likely spread before antibiotic-free feeding in poultry farms. The findings of this study supplement the epidemiological data of salmonellosis and provide an example of the characteristics of Salmonella in the chicken flocks without direct antibiotic selective pressure.

Nontuberculous Mycobacteria in China-incidence and Antimicrobial Resistance Spectrum From a Nationwide Survey

Background: Information on prevalence and resistance spectrum of nontuberculous mycobacteria (NTM) in China is mainly based on regional or local data. A national survey of NTM pulmonary disease was carried out based on acid-fast positive sputum samples collected in 2013.Methods: Sputum samples collected from enrolled presumptive cases were cultured using L-J medium in 72 nationwide tuberculosis surveillance sites from the 31 Chinese mainland provinces and isolates were sent to national tuberculosis reference laboratory (NTRL). The species of re-cultured strains were identified by MALDI-TOF MS and minimal inhibitory concentrations (MICs) were determined to evaluate the drug susceptibility of NTM isolates.Results: Of 4917 mycobacterial isolates cultured, 317 (6.4%, 95% CI, 5.8% to 7.2%) were confirmed as NTM, among which 287 (7.7%, 95% CI, 6.9% to 8.6%) were from the southern region. In inland and coastal China, 87.7% (95% CI, 78.7% to 93.2%) and 50.0% (95% CI, 43.7% to 56.3%) of isolates, respectively, were slow growing mycobacteria (SGM), with the remaining rapid growing mycobacteria (RGM). A total of 29 species were detected, M. abscessus had higher clarithromycin-inducible resistance rates than M. massiliense (65.67% vs 2.22%). M. kansasii was present lower resistance rates in linezolid and moxifloxacin than Mycobacterium avium-intracellulare complex and other SGM.Conclusions: More NTM pulmonary disease was observed in southern and coastal China (p<0.01). SGM was widely distributed, and more RGM are present in southern and coastal China (p<0.01). The antimicrobial resistance spectrum of different NTM species was significant different, accurate species identification would be facilitated to NTM pulmonary disease treatment.