ABSTRACTSince its discovery in the early 2000s, methicillin-resistantStaphylococcus aureus(MRSA) clonal complex 398 (CC398) has become a rapidly emerging cause of human infections, most often associated with livestock exposure. We applied whole-genome sequence typing to characterize a diverse collection of CC398 isolates (n= 89), including MRSA and methicillin-susceptibleS. aureus(MSSA) from animals and humans spanning 19 countries and four continents. We identified 4,238 single nucleotide polymorphisms (SNPs) among the 89 core genomes. Minimal homoplasy (consistency index = 0.9591) was detected among parsimony-informative SNPs, allowing for the generation of a highly accurate phylogenetic reconstruction of the CC398 clonal lineage. Phylogenetic analyses revealed that MSSA from humans formed the most ancestral clades. The most derived lineages were composed predominantly of livestock-associated MRSA possessing three different staphylococcal cassette chromosomemecelement (SCCmec) types (IV, V, and VII-like) including nine subtypes. The human-associated isolates from the basal clades carried phages encoding human innate immune modulators that were largely missing among the livestock-associated isolates. Our results strongly suggest that livestock-associated MRSA CC398 originated in humans as MSSA. The lineage appears to have undergone a rapid radiation in conjunction with the jump from humans to livestock, where it subsequently acquired tetracycline and methicillin resistance. Further analyses are required to estimate the number of independent genetic events leading to the methicillin-resistant sublineages, but the diversity of SCCmecsubtypes is suggestive of strong and diverse antimicrobial selection associated with food animal production.IMPORTANCEModern food animal production is characterized by densely concentrated animals and routine antibiotic use, which may facilitate the emergence of novel antibiotic-resistant zoonotic pathogens. Our findings strongly support the idea that livestock-associated MRSA CC398 originated as MSSA in humans. The jump of CC398 from humans to livestock was accompanied by the loss of phage-carried human virulence genes, which likely attenuated its zoonotic potential, but it was also accompanied by the acquisition of tetracycline and methicillin resistance. Our findings exemplify a bidirectional zoonotic exchange and underscore the potential public health risks of widespread antibiotic use in food animal production.

The molecular processes underlying epidemic waves of methicillin-resistant Staphylococcus aureus (MRSA) are poorly understood1. While a major role has been attributed to the acquisition of virulence determinants by horizontal gene transfer2, there are insufficient epidemiological and functional data supporting that concept. We here report the spread of clones containing a previously extremely rare3,4 mobile genetic element-encoded gene, sasX. We demonstrate that sasX has a key role in MRSA colonization and pathogenesis, significantly enhancing nasal colonization, lung disease, and abscess formation, and promoting mechanisms of immune evasion. Moreover, we observed the recent spread of sasX from sequence type (ST) 239 to invasive clones belonging to other STs. Our study identifies sasX as a quickly spreading critical determinant of MRSA pathogenic success and a promising target for therapeutic interference. Importantly, our results provide proof-of-principle that horizontal gene transfer of key virulence determinants drives MRSA epidemic waves.

is a promising industrial microorganism as well as a major human pathogen. The recent emergence of carbapenem-resistant has posed a serious threat to public health worldwide, emphasizing a dire need for novel therapeutic means against drug-resistant Despite the critical importance of genetics in bioengineering, physiology studies, and therapeutic-means development, genome editing, in particular, the highly desirable scarless genetic manipulation in , is often time-consuming and laborious. Here, we report a two-plasmid system, pCasKP-pSGKP, used for precise and iterative genome editing in By harnessing the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 genome cleavage system and the lambda Red recombination system, pCasKP-pSGKP enabled highly efficient genome editing in using a short repair template. Moreover, we developed a cytidine base-editing system, pBECKP, for precise C→T conversion in both the chromosomal and plasmid-borne genes by engineering the fusion of the cytidine deaminase APOBEC1 and a Cas9 nickase. By using both the pCasKP-pSGKP and the pBECKP tools, the gene was confirmed to be the major factor that contributed to the carbapenem resistance of a hypermucoviscous carbapenem-resistant strain. The development of the two editing tools will significantly facilitate the genetic engineering of Genetics is a key means to study bacterial physiology. However, the highly desirable scarless genetic manipulation is often time-consuming and laborious for the major human pathogen We developed a CRISPR-Cas9-mediated genome-editing method and a cytidine base-editing system, enabling rapid, highly efficient, and iterative genome editing in both industrial and clinically isolated strains. We applied both tools in dissecting the drug resistance mechanism of a hypermucoviscous carbapenem-resistant strain, elucidating that the gene was the major factor that contributed to the carbapenem resistance of the hypermucoviscous carbapenem-resistant strain. Utilization of the two tools will dramatically accelerate a wide variety of investigations in diverse strains and relevant species, such as gene characterization, drug discovery, and metabolic engineering.

Hypervirulent and multidrug resistant Klebsiella pneumoniae strains pose a significant threat to the public health. In the present study, 21 carbapenem-resistant K. pneumoniae isolates (CRKP) were determined by the string test as hypermucoviscous K. pneumoniae (HMKP), with the prevalence of 15.0% (21/140) among CRKP, and 1.1% (21/1838) among all K. pneumoniae isolates. Among them, 7 (33.3%), and 1 (4.76%) isolate belonged to capsular serotype K20 and K2 respectively, while 13 (61.9%, 13/21) weren't successfully typed by capsular serotyping. All the 21 isolates were carbapenemase-producers and were positive for blaKPC-2. In addition to blaKPC-2, all the 21 isolates except one harbor blaSHV-11, and 15 carry extended-spectrum β-lactamase gene blaCTX-M-65. The virulence-associated genes with more than 90% of positive rates among 21 isolates included ureA (100%, 21/21), wabG (100%, 21/21), fimH (95.2%, 20/21), entB (95.2%, 20/21), ycf (95.2%, 20/21), ybtS (95.2%, 20/21), and iutA (90.5%, 19/21). rmpA and aerobactin were found in 57.1% (12/21) isolates. Five sequence types (STs) were identified by multilocus sequence typing (MLST), including ST11 (11 K-non capsule typable and 5 K20 isolates), ST268 (1 K20 isolate and 1 K-non capsule typable isolate), ST65 (1 K2 isolate), ST692 (1 K-non capsule typable isolate), and ST595, a novel sequence type (1 K-non capsule typable isolate). Pulsed-field gel electrophoresis (PFGE) results showed two major PFGE clusters, of which cluster A accounts for 6 ST11 isolates (28.6%) and cluster B includes 8 ST11 isolates (38.1%, 8/21). Ten and six ST11 isolates were isolated from 2014 and 2015, respectively, while 8 were isolated from the same month of December in 2014. Ten isolates were collected from the intensive care unit (ICU), and all except one belonged to ST11. Additional 4 ST11 isolates were collected from patients in non-ICU wards, who had more than 10 days of ICU stay history in 2014 prior to transfer to their current wards where the isolates were recovered. Taken together, the present study showed a hospital outbreak and dissemination of ST11 HMKP with carbapenem resistance caused by KPC-2. Effective surveillance and strict infection control strategies should be implemented to prevent outbreak by HMKP with carbapenem resistance in hospitals.

Between January 2005 and January 2006, 25 (12.8%) of 195 Staphylococcus aureus isolates were positive for Panton-Valentine leukocidin (PVL) genes in a teaching hospital in Wenzhou, China. Nineteen (11.9%) of 160 hospital-acquired isolates, and six (17.1%) of 35 community-acquired isolates, harboured lukS/F-PV. Six sequence types (ST88, ST239, ST398, ST25, ST30 and ST59) were found among 18 PVL-positive methicillin-resistant isolates with SCCmec types I, III, IIIA or IV. Only ST88 was found among seven PVL-positive methicillin-susceptible S. aureus isolates. The PVL-positive isolates were associated with lung infection, bloodstream infection and soft-tissue pyogenic infection. Overall, there was a high prevalence of PVL genes in genetically diverse S. aureus isolates.

A distinctive syndrome caused by hypermucoviscous Klebsiella pneumoniae (HMKP) including pyogenic liver abscess (PLA) is now becoming a globally emerging disease. In the present study, 22.8% (84/369) of K. pneumoniae clinical isolates associated with various types of invasive infections were identified as HMKP, with 45.2% associated with PLA. Multivariate regression analysis showed that male patients with 41–50 years, PLA, diabetes mellitus, and hypertension were independent risk factors for HMKP infections. K2 (42.9%, 36/84) was the most common capsular serotype among HMKP isolates, followed by K1 (23.8%, 20/84). Seventy-five percentage of K1 HMKP isolates were associated with PLA, while K2 HMKP isolates accounted for more types of invasive infections. The positive rates of iutA, mrkD, aerobactin, iroN, and rmpA among HMKP isolates were significantly higher than those among non-HMKP isolates (p < 0.05). There was a correlation between magA, ybtS, alls, and wcaG and K1 isolates. Interestingly, mrkD was exclusively detected among HMKP (32.1%, 27/84) and K2 isolates (65.9%, 27/41). All K1 and K2 HMKP and non-HMKP isolates were positive for rmpA. Aerobactin was found among 95.0 and 97.5% of K1 and K2 isolates. ST23 was found to be the most prevalent ST among 69 HMKP isolates with K1, K2, K5, K20, and K57 (27.5%, 19/69) and was only found among K1 isolates. ST65 was the second most prevalent ST (26.1%, 18/69) and was also only found among K2 isolates. ST23-K1 HMKP isolates (84.2%, 16/19) were associated with PLA, while ST65-K2 isolates were correlated with more types of infections relative to ST23-K1 isolates. PFGE results showed that the homology of 84 HMKP isolates was diverse. Only five PFGE clusters with more than 75% similarity accounted for more than three isolates. These five PFGE clusters only accounted for 35 (41.7%, 35/84) isolates. In conclusion, our study first found that hypertension and male patients with 41–50 years old were independent risk factors. The composition of ST types and PFGE clusters among K. pneumoniae K2 isolates was more diverse than K1 isolates. K1 and K2 HMKP isolates had respective specific profiles of virulence-associated genes.

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Background: Hepatocellular carcinoma (HCC) is one of the most lethal malignancies worldwide. A major cause for the failure of cancer therapy is the development of chemoresistance. Although progress has been made in the study of the mechanisms underlying cancer cells resistance, little is known about the role of microRNAs (miRNAs) in cancer therapy resistance. Methods and Results: Fifteen miRNAs, including 6 up-regulated miRNAs (> 2.0-fold) and 9 down-regulated miRNAs (< 0.5-fold) were differentially expressed in 5-fluorouracil-resistant and their parental cell-lines (HepG2, HepG2/5-FU) by miRNA microarrays. Microarray results were confirmed by validating quantitative real-time polymerase chain reaction (qRT-PCR) analysis. Up-regulation of miR-141 expression resulted in a significant inhibition of 5-FU-mediated cytotoxicity and apoptosis in various hepatocellular carcinoma cells-lines. Mechanically, miR-141 promoted Kelch-like ECH-associated protein 1 (Keap1) mRNA degradation by directly targeting the Keap1 3'untranslated region (3'UTR). Treatment with miR-141 mimics in parental HepG2 cells, restored miR-141 expression and reduced Keap1 levels, thereby resulting in erythroid transcription factor NFE2-L2 (Nrf2) nuclear translocation, activation of Nrf2-dependent HO-1 gene transcription, and subsequent enhancement in 5-FU resistance. Conversely, restoring the expression of Keap1 partly recovered 5-FU sensitivity by counteracting miR-141-mediated 5-FU resistance. Conclusion: Our study showed that miR-141 plays a key role in 5-FU resistance by down-regulating Keap1 expression, thereby reactivating the Nrf2-dependent antioxidant pathway, which may serve as a potential target for overcoming 5-FU resistance in hepatocellular carcinoma cells.