Chromosomal and Plasmid-Borne Tigecycline Resistance Genes tet(X3) and tet(X4) in Dairy Cows on a Chinese Farm.

We isolated 47 Acinetobacter strains carrying tet(X3) and 4 ST767 E. coli strains carrying tet(X4) from 296 rectal swab samples from dairy cows on a Chinese farm. tet(X3) was located on chromosomes or diverse plasmids, and tet(X4) was located on IncFIBκ/FIA(HI1)/X1 nontransferable plasmid. The coexistence of tet(X3) and carbapenemase genes, including blaOXA-58 and blaNDM-1, was detected in 9 Acinetobacter spp. These findings suggested that the use of tetracycline and other antibiotics in food production warrants urgent attention.

Emergence of an Empedobacter falsenii strain harbouring a tet(X)-variant-bearing novel plasmid conferring resistance to tigecycline.

OBJECTIVES: To investigate the genomic and phenotypic characteristics of an MDR Empedobacter falsenii strain isolated from a Chinese patient, which was phenotypically resistant to all last-line antibiotics (carbapenems, colistin and tigecycline). METHODS: Species identity was determined by MALDI-TOF MS analysis. The complete genome sequence of the isolate was determined by WGS and the genetic elements conferring antimicrobial resistance were determined. The origin of this strain was tracked by phylogenetic analysis. RESULTS: The E. falsenii strain was genetically most closely related to an Empedobacter sp. strain isolated from the USA. Members of E. falsenii are speculated to be intrinsically resistant to colistin. The carbapenem resistance of this strain was conferred by a chromosomal blaEBR-2 variant gene. Phylogenetic analysis indicated that the gene encoding the EBR ß-lactamase was widely distributed in Empedobacter spp. Tigecycline resistance was mediated by a tet(X) variant gene encoded by a non-conjugative and non-typeable plasmid. CONCLUSIONS: The MDR phenotype of the E. falsenii isolate was conferred by different mechanisms. Findings from us and others indicate that E. falsenii may serve as a reservoir for carbapenem and tigecycline resistance determinants.

Evolution of Carbapenem-Resistant Serotype K1 Hypervirulent Klebsiella pneumoniae by Acquisition of blaVIM-1-Bearing Plasmid.

We report the identification of a carbapenem-resistant, hypervirulent Klebsiella pneumoniae (hvKp) strain which produced the carbapenemase VIM-1. Genomic analysis showed that the strain belonged to sequence type ST23 and serotype K1, a major hvKp clone, and harbored three resistance-encoding plasmids. Among them, a blaVIM-1-bearing plasmid was found to possess a mosaic structure presumably generated by multiple gene mobilization events. This finding indicates that hvKp actively acquires mobile resistance-encoding elements, facilitating simultaneous expression of hypervirulence and carbapenem-resistance.

Emergence of OXA-232 Carbapenemase-Producing Klebsiella pneumoniae That Carries a pLVPK-Like Virulence Plasmid among Elderly Patients in China.

This study reported the clonal dissemination of OXA-232-producing sequence type 15 (ST15) carbapenem-resistant Klebsiella pneumoniae among elderly patients in China. All patients were immunocompromised, suffered from multiple underlying diseases, and were hospitalized for a prolonged period; however, they slowly recovered on antimicrobial therapy. The blaOXA-232 gene was in a 6.1-kb ColKP3-type nonconjugative plasmid. The strains displayed a multidrug resistance phenotype and were not hypervirulent despite harboring a virulence plasmid. Active surveillance should be enforced to control further transmission.

Rapid Increase in Prevalence of Carbapenem-Resistant Enterobacteriaceae (CRE) and Emergence of Colistin Resistance Gene mcr-1 in CRE in a Hospital in Henan, China.

The global spread of carbapenem-resistant Enterobacteriaceae (CRE) is one of the most severe threats to human health in a clinical setting. The recent emergence of plasmid-mediated colistin resistance gene mcr-1 among CRE strains greatly compromises the use of colistin as a last resort for the treatment of infections caused by CRE. This study aimed to understand the current epidemiological trends and characteristics of CRE from a large hospital in Henan, the most populous province in China. From 2014 to 2016, a total of 7,249 Enterobacteriaceae isolates were collected from clinical samples, among which 18.1% (1,311/7,249) were carbapenem resistant. Carbapenem-resistant Klebsiella pneumoniae and carbapenem-resistant Escherichia coli were the two most common CRE species, with Klebsiella pneumoniae carbapenemases (KPC) and New Delhi metallo-ß-lactamases (NDM), respectively, responsible for the carbapenem resistance of the two species. Notably, >57.0% (n = 589) of the K. pneumoniae isolates from the intensive care unit were carbapenem resistant. Furthermore, blaNDM-5 and mcr-1 were found to coexist in one E. coli isolate, which exhibited resistance to almost all tested antibiotics. Overall, we observed a significant increase in the prevalence of CRE isolates during the study period and suggest that carbapenems may no longer be considered to be an effective treatment for infections caused by K. pneumoniae in the studied hospital.

Population genomic analysis reveals the emergence of high-risk carbapenem-resistant Escherichia coli among ICU patients in China.

OBJECTIVES: The increasing incidence of carbapenem-resistant Enterobacterales (CRE) mediated nosocomial infections has caused a significant public health burden globally. Currently, the prevalence and genomic characteristics of carbapenem-resistant Escherichia coli (CREC) in patients admitted to the intensive care unit (ICU) are unknown. METHODS: Herein, we present a nationwide genomic investigation of CREC isolates among ICU patients in China in 2018 and 2020. In total, 113 CREC isolates were identified from 1105 samples in 25 hospitals, and investigated with phenotyping and genomics approaches. RESULTS: Carbapenemases were produced in 94.69% (107/113) of CREC isolates, which comprise KPC-2 (n = 53, 49.53%), NDM (n = 51, 47.66%), IMP-4 (n = 2, 1.87%), and OXA-181 (n = 1, 0.93%). Notably, CREC isolates co-carrying mcr-9 and blaNDM-5 or tet(X4) and blaNDM-5 were first identified in clinical settings. The carbapenemase genes of most isolates were located on the plasmids. The blaKPC gene was mainly mediated by IncFII plasmids (n = 37, 69.81%), and blaNDM was located on the IncX3 plasmid (n = 36, 70.59%). CREC isolates belonged to diverse sequence types (STs) of which ST131 was the most prevalent blaKPC-positive CREC isolates (34/113, 30.09%), while blaNDM was associated with ST617 and ST410 isolates, thereby indicating that multiple CREC clones spread in Chinese ICU patients. CONCLUSIONS: This study highlights the emerging threat of high-risk CREC isolates such as ST131 circulating in the ICU in China. Hence, stringent monitoring of such high-risk clones should be performed.

Increased clonal dissemination of OXA-232-producing ST15 Klebsiella pneumoniae in Zhejiang, China from 2018 to 2021.

BACKGROUND: OXA-232-producing Klebsiella pneumoniae was first identified in China in 2016, and its clonal transmission was reported in 2019. However, there are no prevalence and genotypic surveillance data available for OXA-232 in China. Therefore, we investigated the trends and characteristics of OXA-232 type carbapenemase in Zhejiang Province, China from 2018 to 2021. METHODS: A total of 3278 samples from 1666 patients in the intensive care units were collected from hospitals in Zhejiang Province from 2018 to 2021. Carbapenem-resistant isolates were initially selected by China Blue agar plates supplemented with 0.3 µg/ml meropenem, and further analyzed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry identification, immune colloidal gold technique, conjugation experiment, antimicrobial susceptibility testing and whole genome sequencing. RESULTS: A total of 79 OXA-producing strains were recovered, with the prevalence increased from 1.8% [95% confidence interval (CI): 0.7-3.7%] in 2018 to 6.0% (95% CI: 4.4-7.9%) in 2021. Seventy-eight strains produced OXA-232 and one produced OXA-181. The blaOXA-232 gene in all strains was located in a 6141-bp ColKP3-type non-conjugative plasmid and the blaOXA-181 gene was located in a 51,391-bp ColKP3/IncX3-type non-conjugative plasmid. The blaOXA-232-producing K. pneumoniae was dominated (75/76) by isolates of sequence type 15 (ST15) that differed by less than 80 SNPs. All OXA-producing strains (100%, 95% CI: 95.4-100.0%) were multidrug-resistant. CONCLUSIONS: From 2018 to 2021, OXA-232 is the most prevalent OXA-48-like derivative in Zhejiang Province, and ST15 K. pneumoniae isolates belonging to the same clone are the major carriers. The transmission of ColKP3-type plasmid to E. coli highlighted that understanding the transmission mechanism is of great importance to delay or arrest the propagation of OXA-232 to other species.

Prevalence, transmission, and molecular epidemiology of tet(X)-positive bacteria among humans, animals, and environmental niches in China: An epidemiological, and genomic-based study.

Plasmid-mediated, transmissible, tigecycline-inactivating enzyme Tet(X) has attracted considerable public attention. However, so far studies have not addressed its impact on public health and the ecosystem. Herein, we report the prevalence and molecular epidemiology of tet(X)-positive bacteria (TPB) from diverse sources, investigate the host-specificity of TPB and the transferability of tet(X). Sample collection was conducted between 2018 and 2020 in 30 provinces in China. PCR screening suggested tet(X) was prevalent among freshwater fishes (24.7%, 95% CI 19.4-30.7%), followed by chickens (23.6%, 21.2-26.2%), cattle (19.3%, 16.4-22.5%), healthy individuals (6.2%, 5.4-7.1%), and patients (0.3%, 0.0-1.1%). Soil and freshwater samples all tested negative for tet(X). A total of 289 TPB were isolated from 7516 samples (120/1181 chicken, 82/669 cattle, 68/3229 healthy individual, 17/239 freshwater fish and 2/2121 clinical samples). TPB distributed in six major families of bacteria including Moraxellaceae (n = 99, 34.3%), Flavobacteriaceae (n = 95, 32.9%), Enterobacteriaceae (n = 83, 28.7%), Pseudomonadaceae (n = 9, 3.1%), Sphingobacteriaceae (n = 2, 0.7%) and unclassified Gammaproteobacteria (n = 1, 0.3%). Diverse tet(X) genes including tet(X2), tet(X3), tet(X4), tet(X5) and tet(X6) were identified from different TPB. The tet(X)-positive bacteria were highly diverse, with ST10 complex belonging to the dominant E. coli clone. Novel hosts of tet(X) including Enterobacter hormaechei, Ignatzschineria indica and Oblitimonas alkaliphila were identified. Isolates from different families exhibited different antimicrobial resistance profiles. Co-existence of tet(X) with other resistance genes such as floR (66.8%) and carbapenemase genes (33.2%) was commonly observed. tet(X) could be transferred among E. coli isolates at frequencies from 10-4 to 10-10. Species other than E. coli failed to transfer tet(X) gene to the E. coli recipient via conjugation. Discriminant analysis of principal components analysis suggested inter-host transmission of tet(X)-positive E. coli among diverse hosts was not observed. Future studies are needed to monitor the transmission trend as well as the impact of this resistance gene in clinical infection control.

Clinical evolution of ST11 carbapenem resistant and hypervirulent Klebsiella pneumoniae.

Carbapenem-resistant and hypervirulent K. pneumoniae (CR-HvKP) strains that have emerged recently have caused infections of extremely high mortality in various countries. In this study, we discovered a conjugative plasmid that encodes carbapenem resistance and hypervirulence in a clinical ST86 K2 CR-HvKP, namely 17ZR-91. The conjugative plasmid (p17ZR-91-Vir-KPC) was formed by fusion of a non-conjugative pLVPK-like plasmid and a conjugative blaKPC-2-bearing plasmid and is present dynamically with two other non-fusion plasmids. Conjugation of p17ZR-91-Vir-KPC to other K. pneumoniae enabled them to rapidly express the carbapenem resistance and hypervirulence phenotypes. More importantly, genome analysis provided direct evidence that p17ZR-91-Vir-KPC could be directly transmitted from K2 CR-HvKP strain, 17ZR-91, to ST11 clinical K. pneumoniae strains to convert them into ST11 CR-HvKP strains, which explains the evolutionary mechanisms of recently emerged ST11 CR-HvKP strains.

Colistin-resistance gene mcr in clinical carbapenem-resistant Enterobacteriaceae strains in China, 2014-2019.

To investigate whether introduction of colistin into the clinical settings selected colistin-resistant CRE, we performed molecular epidemiological study of 1868 CRE strains collected from different geographical locales in China during the period 2014-2019. 1755 (96.18%) isolates carried the carbapenemase genes blaKPC and blaNDM; 14 Escherichia coli isolates (0.75%) carrying mcr-1 and blaNDM (MCR-CREC) were also identified. Importantly, the number and relative prevalence of MCR-CREC isolates increased from 5 (0.41%) to 9 (1.38%) after introduction of polymyxin into clinical practice. Consistently, results of genetic analysis indicated that MCR-CREC strains collected before December 2017 were genetically diverse, yet those collected after that date exhibited more closely related genetic profiles, indicating that specific MCR-CREC strains were rapidly selected as a result of increased usage of colistin in clinical settings. The resistance level of MCR-CREC isolates to colistin increased after the introduction of polymyxin into clinical use with the MIC to colistin from <2 mg/L in 80% strains to 2 mg/L in 100% strains. Further dissemination of MCR-CREC strains, which exhibit resistance to the last-line drugs of carbapenems and colistin, is expected to pose a severe threat to human health.

Conjugation of Virulence Plasmid in Clinical Klebsiella pneumoniae Strains through Formation of a Fusion Plasmid.

The rapid dissemination of non-conjugative virulence plasmids among non-K1/K2 types of Klebsiella pneumoniae poses an unprecedented threat to human health, yet the underlying mechanisms governing dissemination of such plasmids is unclear. In this study, a novel 68 581 bp IncFIA plasmid is discovered that can be fused to a hypervirulence-encoding plasmid to form a hybrid conjugative virulence plasmid in conjugation experiments; such fusion events involve homologous recombination between a 241 bp homologous region located in each of the two plasmids. The fusion hypervirulence-encoding plasmid can be conjugated to both classic and blaKPC-2 -bearing carbapenem-resistant K. pneumoniae strains through conjugation, enabling such strains to acquire the ability to express the hypervirulence phenotype. Dissemination of this fusion virulence plasmid will impose an enormous burden on current efforts to control and treat infections caused by multidrug resistant and hypervirulent K. pneumoniae.

Dynamic Colonization of Klebsiella pneumoniae Isolates in Gastrointestinal Tract of Intensive Care Patients.

Gastrointestinal carriage is regarded as a major reservoir of K. pneumoniae infections, especially in intensive care patients. A total of 101 (95.3%) KPC-producing carbapenem-resistant K. pneumoniae (CRKP) isolates were identified among 106 CRKP isolates collected from stool samples of inpatients performing active rectal screening for carbapenem-resistant Enterobacteriaceae during hospitalization in the ICUs of a tertiary hospital between 2016 and 2017. Among them, six KPC-producing CRKP isolates from three patients (two isolates for each patient) were identified with distinct antibacterial susceptibility. Our findings showed that: (1) bla KPC-2 gene is predominant in CRKP strains isolated from the intensive care patients and can be incorporated into various plasmids that are transmissible among multiple bacterial hosts in the human gastrointestinal tract; (2) the human gastrointestinal tract has a capacity to dynamically colonize multiple clones of CRKP strains with varied plasmids, diverse antimicrobial resistance genes and virulence genes. K. pneumoniae colonization is an important step in progression to extraintestinal infection, which provides the rationale for establishing intervention measures to prevent subsequent infection. Thus, close surveillance on CRKP colonization, together with effective infection prevention and control measures, should be put into practice.

Leclercia adecarboxylata From Human Gut Flora Carries mcr-4.3 and bla IMP-4-Bearing Plasmids.

A clinical Leclercia adecarboxylata strain harboring the mcr-4.3 and bla IMP-4 genes was isolated from active rectal screening of carbapenem-resistant Enterobacteriaceae (CRE) in a patient. The isolate was found to harbor seven plasmids, including a 94,635 bp bla IMP-4-bearing IncN plasmid and a 9,782 bp mcr-4.3-bearing ColE10-type plasmid. The isolate was susceptible to colistin despite carrying the mcr-4.3 gene, suggesting that this MCR-4 variant may not be functional. Carriage of antibiotic resistance genes in human gut L. adecarboxylata strain suggests that close surveillance of resistance strains in the human gut flora should be included as a routine clinical practice to prevent occurrence of infections, especially among immunocompromised patients.

Prevalence and phenotypic characterization of carbapenem-resistant Klebsiella pneumoniae strains recovered from sputum and fecal samples of ICU patients in Zhejiang Province, China.

OBJECTIVE: To understand the prevalence and transmission of carbapenem-resistant Klebsiella pneumoniae (CRKP) in ICU patients in Zhejiang Province, China, and determined the genetic and phenotypic characteristics of these CRKP strains. MATERIALS AND METHODS: A total of 202 ICU patients from eight tertiary hospitals were recruited and 55 non-duplicate CRKP strains were collected during July and August in 2017. These strains were subjected to determination of MICs, carriage of carbapenemase genes and tet(A) variants, PFGE, MLST and virulence potential using G. mellonella larvae infection model. RESULTS: A total of 55 CRKP strains were recovered from 42 patients, representing a carriage rate of 20.8%. CRKP strains were recovered from both the intestinal and respiratory tract of 13 patients. Importantly, strains isolated from sputum and fecal samples often displayed identical PFGE profiles, suggesting that CRKP may also colonize the respiratory tract. The most dominant ST type of these CRKP strains was ST11, accounting for 78% (43/55) of the test strains. The majority of CRKP strains were resistant to multiple antibiotics, with the exception of tigecycline and ceftazidime/avibactam. Interestingly, 32 strains were found to harbor the tet(A) variant, which is known to confer reduced tigecycline susceptibility. Assessment of the virulence potential of these CRKP strains by string test showed that results were negative for 53 of the 55 test strains. However, further assessment of virulence potential using a G. mellonella larvae infection model showed that CRKP isolated from sputum consistently exhibited a higher virulence level than strains recovered from fecal samples. CONCLUSION: CRKP is highly prevalent in ICU patients in Zhejiang Province with strains isolated from respiratory exhibiting higher virulence potential than those from GI tract. These data provide essential insight into development of new infection control measures to halt the transmission of CRKP in clinical settings.

Alkaline Peptone Water-Based Enrichment Method for mcr-3 From Acute Diarrheic Outpatient Gut Samples.

A third plasmid-mediated colistin resistance gene, mcr-3, is increasingly being reported in Enterobacteriaceae and Aeromonas spp. from animals and humans. To investigate the molecular epidemiology of mcr in the gut flora of Chinese outpatients, 152 stool specimens were randomly collected from outpatients in our hospital from May to June, 2017. Stool specimens enriched in alkaline peptone water or Luria-Bertani (LB) broth were screened for mcr-1, mcr-2, and mcr-3 using polymerase chain reaction (PCR)-based assays. Overall, 19.1% (29/152) and 5.3% (8/152) of the stool samples enriched in alkaline peptone water were PCR-positive for mcr-1 and mcr-3, respectively, while 2.7% (4/152) of samples were positive for both mcr-1 and mcr-3. Strains isolated from the samples that were both mcr-1- and mcr-3-positive were subjected to antimicrobial susceptibility testing by broth microdilution. They were also screened for the presence of other resistance genes by PCR, while multilocus sequence typing and whole-genome sequencing were used to investigate the molecular epidemiology and genetic environment, respectively, of the resistance genes. mcr-3-positive Aeromonas veronii strain 126-14, containing a mcr-3.8-mcr-3-like2 segment, and mcr-1-positive Escherichia coli strain 126-1, belonging to sequence type 1485, were isolated from the sample from a diarrheic butcher with no history of colistin treatment. A. veronii 126-14 had a colistin minimum inhibitory concentration (MIC) of 2 µg/mL and was susceptible to antibiotics in common use, while E. coli 126-1 produced TEM-1, CTX-M-55, and CTX-M-14 ß-lactamases and was resistant to colistin, ceftazidime, and cefotaxime. Overall, there was a higher detection rate of mcr-3-carrying strains with low colistin MICs from the samples enriched in alkaline peptone water than from samples grown in LB broth.

Emerging Carriage of NDM-5 and MCR-1 in Escherichia coli From Healthy People in Multiple Regions in China: A Cross Sectional Observational Study.

BACKGROUND: Carriage of carbapenem-resistant Enterobacteriaceae (CRE) in humans may contribute to the dissemination of CRE and impact on communities and healthcare facilities. Carbapenem-resistant Escherichia coli (CREC) is one of the major type of CRE in the human gut. Here, we describe a cross-sectional study to investigate the prevalence of CREC, and in particular the mcr-1 carrying CREC, in health volunteers in China. METHODS: During September to December 2016, 3859 non-duplicated stool specimens were collected from healthy volunteers who received regular physical examinees in healthcare centers located in 19 provinces across China. Enrichment culture supplemented meropenem was used to isolate CREC. Carbapenemase producing determinants and the mcr-1 gene were determined by PCR amplification and sequencing. Isolates were further analyzed by antibiotic susceptibility test, genotyping, and whole genome analysis. FINDINGS: A total of 92 non-duplicated CREC were isolated from 3859 stool specimens, among which 43 CREC are carbapenemase positive. In addition, the co-existence of bla NDM and mcr-1 was found in 14 CREC, which also showed resistance to the majority of all antimicrobial agents analyzed. The genetic background of these CREC isolates are highly diversified based on molecular typing. Furthermore, whole genome sequence indicated that NDM-5 is the predominant determinant conferring carbapenem resistance in CREC, and that NDM-5 carrying plasmids (IncX3) are very similar. INTERPRETATION: The incidence of CREC carriage in healthy people in China was small; however, the co-existence of CREC with mcr-1 is disconcerting. Therefore, pre-screening prior to admission and monitoring of patients on high-dependency wards is highly recommended to control and prevent the dissemination of CRE in hospitals. OUTSTANDING QUESTION: The high prevalence of CREC in the healthy people should not be underestimated, as it may increase the risk of infection. This knowledge could have impact on the pre-screening and monitoring of CRE before patient administration.

A fatal outbreak of ST11 carbapenem-resistant hypervirulent Klebsiella pneumoniae in a Chinese hospital: a molecular epidemiological study.

BACKGROUND: Hypervirulent Klebsiella pneumoniae strains often cause life-threatening community-acquired infections in young and healthy hosts, but are usually sensitive to antibiotics. In this study, we investigated a fatal outbreak of ventilator-associated pneumonia caused by a new emerging hypervirulent K pneumoniae strain. METHODS: The outbreak occurred in the integrated intensive care unit of a new branch of the Second Affiliated Hospital of Zhejiang University (Hangzhou, China). We collected 21 carbapenem-resistant K pneumoniae strains from five patients and characterised these strains for their antimicrobial susceptibility, multilocus sequence types, and genetic relatedness using VITEK-2 compact system, multilocus sequence typing, and whole genome sequencing. We selected one representative isolate from each patient to establish the virulence potential using a human neutrophil assay and Galleria mellonella model and to establish the genetic basis of their hypervirulence phenotype. FINDINGS: All five patients had undergone surgery for multiple trauma and subsequently received mechanical ventilation. The patients were aged 53-73 years and were admitted to the intensive care unit between late February and April, 2016. They all had severe pneumonia, carbapenem-resistant K pneumoniae infections, and poor responses to antibiotic treatment and died due to severe lung infection, multiorgan failure, or septic shock. All five representative carbapenem-resistant K pneumoniae strains belonged to the ST11 type, which is the most prevalent carbapenem-resistant K pneumoniae type in China, and originated from the same clone. The strains were positive on the string test, had survival of about 80% after 1 h incubation in human neutrophils, and killed 100% of wax moth larvae (G mellonella) inoculated with 1 × 106 colony-forming units of the specimens within 24 h, suggesting that they were hypervirulent K pneumoniae. Genomic analyses showed that the emergence of these ST11 carbapenem-resistant hypervirulent K pneumoniae strains was due to the acquisition of a roughly 170 kbp pLVPK-like virulence plasmid by classic ST11 carbapenem-resistant K pneumoniae strains. We also detected these strains in specimens collected in other regions of China. INTERPRETATION: The ST11 carbapenem-resistant hypervirulent K pneumoniae strains pose a substantial threat to human health because they are simultaneously hypervirulent, multidrug resistant, and highly transmissible. Control measures should be implemented to prevent further dissemination of such organisms in the hospital setting and the community. FUNDING: Chinese National Key Basic Research and Development Program and Collaborative Research Fund of Hong Kong Research Grant Council.