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Tuberculosis among Tibetans increased in New York City between 1995 and 1999. We examined characteristics of 68 Tibetan patients compared to 702 non-Tibetan patients from Nepal, India, or China, diagnosed between January 1995 and December 1999. The number of Tibetan patients increased each year after 1995 whereas non-Tibetans remained stable during the same period. Tibetans were younger (27 vs. 44 years), more likely to be infectious (63% vs. 46%), have multidrug resistance (7% vs. 2%) and shorter time to diagnosis after arrival (9 vs. 79 months, p < 0.01). For Tibetan patients, 68% of identified contacts were evaluated. The prevalence of tuberculosis infection was 65%. In contrast, among non-Tibetan patients 88.8% of contacts were evaluated and 45.2% were infected. Outreach efforts with community leaders and educational presentations at community events have been implemented in an effort to ensure continuity of care and completion of treatment. [ABSTRACT FROM AUTHOR]

Background: Mobile plasmids play a key role in spurring the global dissemination of multidrug-resistant (MDR) K. pneumoniae, while plasmid curing has been recognized as a promising strategy to combat antimicrobial resistance. Here we exploited a K. pneumoniae native CRISPR system to cure the high-risk IncFII plasmids., Methods: We examined matched protospacers in 725 completely sequenced IncFII plasmids from K. pneumoniae genomes. Then, we re-engineered a native CRISPR-Cas3 system and deliver the CRISPR-Cas3 system via conjugation. Plasmid killing efficiency and G. mellonella infection model were applied to evaluate the CRISPR-Cas3 immunity in vitro and in vivo., Findings: Genomic analysis revealed that most IncFII plasmids could be targeted by the native CRISPR-Cas3 system with multiple matched protospacers, and the targeting regions were highly conserved across different IncFII plasmids. This conjugative endogenous CRISPR-Cas3 system demonstrated high plasmid curing efficiency in vitro (8-log decrease) and in vivo (∼100% curing) in a Galleria mellonella infection model, as well as provided immunization against the invasion of IncFII plasmids once the system entering a susceptible bacterial host., Interpretation: Overall, our work demonstrated the applicability of using native CRISPR-mediated plasmid curing to re-sensitize drug-resistant K. pneumoniae to multiple antibiotics. This work provided strong support for the idea of utilizing native CRISPR-Cas systems to tackle AMR in K. pneumoniae., Funding: This work was supported by research grants National Natural Science Foundation of China [grant numbers 81871692, 82172315, 82102439, and 82202564], the Shanghai Science and Technology Commission [grant number 19JC1413002], and Shanghai Sailing Program [grant number 22YF1437500]., Competing Interests: Declaration of interests None to declare., (Copyright © 2023. Published by Elsevier B.V.)

Background: The recent emergence and dissemination of high-level mobile tigecycline resistance Tet(X) challenge the clinical effectiveness of tigecycline, one of the last-resort therapeutic options for complicated infections caused by multidrug-resistant Gram-negative and Gram-positive pathogens. Although tet(X) has been found in various bacterial species, less is known about phylogeographic distribution and phenotypic variance of different genetic variants., Methods: Herein, we conducted a multiregional whole-genome sequencing study of tet(X)-positive Acinetobacter isolates from human, animal, and their surrounding environmental sources in China. The molecular and enzymatic features of tet(X) variants were characterized by clonal expression, microbial degradation, reverse transcription, and gene transfer experiments, while the tet(X) genetic diversity and molecular evolution were explored by comparative genomic and Bayesian evolutionary analyses., Results: We identified 193 tet(X)-positive isolates from 3846 samples, with the prevalence ranging from 2.3 to 25.3% in nine provinces in China. The tet(X) was broadly distributed in 12 Acinetobacter species, including six novel species firstly described here. Besides tet(X3) (n = 188) and tet(X4) (n = 5), two tet(X5) variants, tet(X5.2) (n = 36) and tet(X5.3) (n = 4), were also found together with tet(X3) or tet(X4) but without additive effects on tetracyclines. These tet(X)-positive Acinetobacter spp. isolates exhibited 100% resistance rates to tigecycline and tetracycline, as well as high minimum inhibitory concentrations to eravacycline (2-8 μg/mL) and omadacycline (8-16 μg/mL). Genetic analysis revealed that different tet(X) variants shared an analogous ISCR2-mediated transposon structure. The molecular evolutionary analysis indicated that Tet(X) variants likely shared the same common ancestor with the chromosomal monooxygenases that are found in environmental Flavobacteriaceae bacteria, but sequence divergence suggested separation ~ 9900 years ago (7887 BC), presumably associated with the mobilization of tet(X)-like genes through horizontal transfer., Conclusions: Four tet(X) variants were identified in this study, and they were widely distributed in multiple Acinetobacter spp. strains from various ecological niches across China. Our research also highlighted the crucial role of ISCR2 in mobilizing tet(X)-like genes between different Acinetobacter species and explored the evolutionary history of Tet(X)-like monooxygenases. Further studies are needed to evaluate the clinical impact of these mobile tigecycline resistance genes.

Tigecycline serves as one of the antibiotics of last resort to treat multidrug-resistant (including carbapenem-resistant) pathogens. However, the recently emerged plasmid-mediated tigecycline resistance mechanism, Tet(X), challenges the clinical efficacy of this class of antibiotics. In this study, we detected 180 tet (X)-harboring Acinetobacter isolates (8.9%, n  = 180) from 2,018 samples collected from avian farms and adjacent environments in China. Eighteen tet (X)-harboring isolates (10.0%) were found to cocarry the carbapenemase gene bla NDM-1 , mostly from waterfowl samples (94.4%, 17/18). Interestingly, among six Acinetobacter strains, tet (X) and bla NDM-1 were found to colocalize on the same plasmids. Moreover, whole-genome sequencing (WGS) revealed a novel orthologue of tet (X) in the six isolates coharboring tet (X) and bla NDM-1 Inverse PCR suggested that the two tet (X) genes form a single transposable unit and may be cotransferred. Sequence comparison between six tet (X)- and bla NDM-1 -coharboring plasmids showed that they shared a highly homologous plasmid backbone even though they were isolated from different Acinetobacter species (three from Acinetobacter indicus , two from Acinetobacter schindleri species in China. Emergence and spread of such plasmids and strains are of great clinical concern, and measures must be implemented to avoid their dissemination.Acinetobacter lwoffii ) from various sources and from different geological regions, suggesting the horizontal genetic transfer of a common tet (X)- and bla NDM-1 -coharboring plasmid among Acinetobacter species in China. Emergence and spread of such plasmids and strains are of great clinical concern, and measures must be implemented to avoid their dissemination., (Copyright © 2020 American Society for Microbiology.)

Tigecycline is one of the last-resort antibiotics to treat complicated infections caused by both multidrug-resistant Gram-negative and Gram-positive bacteria 1 . Tigecycline resistance has sporadically occurred in recent years, primarily due to chromosome-encoding mechanisms, such as overexpression of efflux pumps and ribosome protection 2,3 . Here, we report the emergence of the plasmid-mediated mobile tigecycline resistance mechanism Tet(X4) in Escherichia coli isolates from China, which is capable of degrading all tetracyclines, including tigecycline and the US FDA newly approved eravacycline. The tet(X4)-harbouring IncQ1 plasmid is highly transferable, and can be successfully mobilized and stabilized in recipient clinical and laboratory strains of Enterobacteriaceae bacteria. It is noteworthy that tet(X4)-positive E. coli strains, including isolates co-harbouring mcr-1, have been widely detected in pigs, chickens, soil and dust samples in China. In vivo murine models demonstrated that the presence of Tet(X4) led to tigecycline treatment failure. Consequently, the emergence of plasmid-mediated Tet(X4) challenges the clinical efficacy of the entire family of tetracycline antibiotics. Importantly, our study raises concern that the plasmid-mediated tigecycline resistance may further spread into various ecological niches and into clinical high-risk pathogens. Collective efforts are in urgent need to preserve the potency of these essential antibiotics.

We isolated a New Delhi metallo-β-lactamase 5 (NDM-5)-producing Klebsiella pneumoniae sequence type (ST) 258 strain in southwest China during 2017. The bla NDM-5 gene was acquired by horizontal plasmid transfer from NDM-5-producing Escherichia coli. We identified genomic characteristics in ST258 strains that differed from those of global K. pneumoniae carbapenemase-producing strains.

Plasmid-mediated antimicrobial resistance has emerged as one of the principal global issues, posing significant threats to public health. Herein, we reported a mobile tigecycline resistance mechanism Tet(X4) on both plasmid and chromosome in Escherichia coli strains from migratory birds in China. Besides tigecycline, these tet (X4)-positive strains also exhibited elevated MICs to the FDA newly approved tetracycline antibiotics, eravacycline (4 µg/ml) and omadacycline (8 µg/ml). Worrisomely, the tet (X4)-carrying plasmids and chromosome also shared high homology with the plasmids from human. Taken together, Tet(X4) represents another emerging antimicrobial threat and collective efforts from different sectors are needed to control its further spread.

We describe the first report of a clinical colistin-resistant ST84 Enterobacter cloacae isolate coharboring mcr-4.3 (previously named mcr-4.2 ) and bla from a patient in China. The NDM-1 from a patient in China. The bla NDM-1 -harboring IncX3 plasmid and the novel mcr-4.3 -harboring ColE plasmid were completely sequenced. Although this isolate showed a high level of resistance to colistin, mcr-4.3 plasmid transformation, gene subcloning, susceptibility testing, and lipid A matrix-assisted laser desorption ionization mass spectrometry analysis indicated that mcr-4.3 itself does not confer resistance to colistin., (Copyright © 2018 American Society for Microbiology.)

Carbapenem-resistant and hypervirulent Klebsiella pneumoniae strains have emerged recently. These strains are both hypervirulent and multidrug resistant and may also be highly transmissible and able to cause severe infections in both the hospital and the community. Clinical and public health needs require a rapid and comprehensive molecular detection assay to identify and track the spread of these strains and provide timely infection control information. Here, we develop a rapid multiplex PCR assay capable of distinguishing K. pneumoniae carbapenem-resistant isolates of sequence type 258 (ST258) and ST11, and hypervirulent ST23, ST65/ST375, and ST86 clones, as well as capsular types K1, K2, K locus type 47 (KL47), and KL64, and virulence genes rmpA , rmpA2 , iutA , and iroN The assay demonstrated 100% concordance with 118 previously genotyped K. pneumoniae isolates and revealed different populations of carbapenem-resistant and hypervirulent strains in two collections in China and the United States. The results showed that carbapenem-resistant and hypervirulent K. pneumoniae strains are still rare in the United States, whereas in China, ∼50% of carbapenem-resistant strains carry rmpA/rmpA2 and iutA virulence genes, which are largely associated with the epidemic ST11 strains. Similarly, a high prevalence of hypervirulent strains was found in carbapenem-susceptible isolates in two Chinese hospitals, but these primarily belong to ST23, ST65/ST375, and ST86, which are distinct from the carbapenem-resistant strains. Taken together, our results demonstrated that this PCR assay can be a useful tool for molecular surveillance of carbapenem-resistant and hypervirulent K. pneumoniae strains., (Copyright © 2018 American Society for Microbiology.)

Next-generation sequencing of 6 mcr-1 -harboring Escherichia coli and Klebsiella pneumoniae isolates collected from a tertiary care hospital in China revealed significant sequence variations in the regions flanking the mcr-1 gene. While sequence variations significantly affected the expression and promoter activity of mcr-1 , the mcr-1 gene expression levels did not correlate with the in vitro colistin resistance levels, which warrants further in-depth investigations., (Copyright © 2018 American Society for Microbiology.)

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 bla KPC-2 . In addition to bla KPC-2 , all the 21 isolates except one harbor bla SHV-11 , and 15 carry extended-spectrum β-lactamase gene bla CTX-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.

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.

Since the first report of bla NDM-1 , 16 bla NDM variants have been identified among Gram-negative bacteria worldwide. Recently, a novel bla NDM variant, bla ST5138 clinical isolate associated with hospital-acquired urinary tract infection from China. NDM-13 , was identified in the chromosome of an ST101 Escherichia coli isolate from Nepal. Here we first reported plasmid-mediated bla NDM-13 in a carbapenem-resistant E. coli -harboring vector circulating in China. In accordance with the structure of pNDM-HN380, pNDM13-DC33 consists of a 33-kb backbone encoding plasmid replication ( bla NDM-13 and bla SHV-12 coexisted on the a ~54 Kb self-transferable plasmid. Compared with NDM-1, NDM-13, NDM-3, and NDM-4 had two amino acid substitutions (D95N and M154L), one amino acid substitution (D95N) and one amino acid substitutions (M154L), respectively. Complete plasmid sequencing showed that bla NDM-13 -harboring plasmid (pNDM13-DC33) was highly similar to the bla NDM-1 -harboring IncX3 plasmid pNDM-HN380, a common bla NDM -harboring vector circulating in China. In accordance with the structure of pNDM-HN380, pNDM13-DC33 consists of a 33-kb backbone encoding plasmid replication ( repB ), stability partitioning, and transfer ( tra, trb , and pil ) functions, and a 21-kb antimicrobial resistance region with high GC content between umuD and mpr genes. In conclusion, the present study is the first report of a plasmid-encoded bla NDM-13 and the complete sequence of a bla NDM-13 -harboring plasmid (pNDM13-DC33). bla NDM-13 maybe originate from bla NDM-1 located on a pNDM-HN380-like plasmid by sequential mutations.

The spread of the plasmid-mediated colistin resistance gene, mcr-1, into carbapenem-resistant Enterobacteriaceae (CRE) clinical isolates poses a significant threat to global health. Here we report the identification of three mcr-1-harboring carbapenem-resistant Escherichia coli strains, collected from three patients in two provinces in China. Our results show that mcr-1-harboring CRE strains have started to spread in different hospitals in China. In addition, this report presents the first description of chromosomal integration of mcr-1 into a carbapenem-resistant E. coli strain., (Copyright © 2016, American Society for Microbiology. All Rights Reserved.)

We report here the nucleotide sequence of a novel blaKPC-2-harboring incompatibility group N (IncN) plasmid, pECN580, from a multidrug-resistant Escherichia coli sequence type 131 (ST131) isolate recovered from Beijing, China. pECN580 harbors β-lactam resistance genes blaKPC-2, blaCTX-M-3, and blaTEM-1; aminoglycoside acetyltransferase gene aac(6')-Ib-cr; quinolone resistance gene qnrS1; rifampin resistance gene arr-3; and trimethoprim resistance gene dfrA14. The emergence of a blaKPC-2-harboring multidrug-resistant plasmid in an epidemic E. coli ST131 clone poses a significant potential threat in community and hospital settings.

Targeted IS6110-based RFLP genotyping can be applied to rapidly identify specific groups of biomedically/epidemiologically relevant Mycobacterium tuberculosis clinical isolates. One such group is the W-Beijing strain family (also known as Beijing/W), implicated in significant nosocomial and community outbreaks worldwide. Using previously defined criteria, we developed a simple and accurate method to identify members of the W-Beijing family, based on rehybridization of Southern blot membranes used previously in routine IS6110 DNA fingerprint analysis. The hybridization probe constructed ("W-Beijing polyprobe") contains the PCR-amplified fragments specific for three M. tuberculosis chromosomal loci used for the identification of W-Beijing strains. The targets include the dnaA-dnaN and NTF regions and the direct repeat locus. A total of 526 selected clinical isolates (representative of 253 different IS6110-defined strain types) were analyzed using the W-Beijing polyprobe. A total of 148 isolates from this collection were found to be members of the W-Beijing phylogenetic lineage, comprising 106 strains from the W-Beijing family (46 clusters) and 42 related isolates. Rehybridization results were confirmed by computer-assisted analysis. The sensitivity and specificity of this method were estimated at 98.7% and 99.7%, respectively. This study demonstrates that the W-Beijing polyprobe can accurately and reliably discriminate members of the W-Beijing phylogenetic lineage and the W-Beijing family of M. tuberculosis strains.

Mycobacterium tuberculosis Beijing genotype strains are highly prevalent in Asian countries and in the territory of the former Soviet Union. They are increasingly reported in other areas of the world and are frequently associated with tuberculosis outbreaks and drug resistance. Beijing genotype strains, including W strains, have been characterized by their highly similar multicopy IS6110 restriction fragment length polymorphism (RFLP) patterns, deletion of spacers 1 to 34 in the direct repeat region (Beijing spoligotype), and insertion of IS6110 in the genomic dnaA-dnaN locus. In this study the suitability and comparability of these three genetic markers to identify members of the Beijing lineage were evaluated. In a well-characterized collection of 1,020 M. tuberculosis isolates representative of the IS6110 RFLP genotypes found in The Netherlands, strains of two clades had spoligotypes characteristic of the Beijing lineage. A set of 19 Beijing reference RFLP patterns was selected to retrieve all Beijing strains from the Dutch database. These reference patterns gave a sensitivity of 98.1% and a specificity of 99.7% for identifying Beijing strains (defined by spoligotyping) in an international database of 1,084 strains. The usefulness of the reference patterns was also assessed with large DNA fingerprint databases in two other European countries and for identification strains from the W lineage found in the United States. A standardized definition for the identification of M. tuberculosis strains belonging to the Beijing/W lineage, as described in this work, will facilitate further studies on the spread and characterization of this widespread genotype family of M. tuberculosis strains.