High incidence and endemic spread of NDM-1-positive Enterobacteriaceae in Henan Province, China

Shift in the dominant sequence type of carbapenem-resistant Klebsiella pneumonia infection from ST278-NDM-1 to ST11-KPC-2 in neonatal patients in a children's hospital in Shanghai, China, 2017-2021

OBJECTIVES

To investigate the clinical characteristics and molecular epidemiology of CRKP infection in neonatal patients in a children's hospital in China from 2017 to 2021.

METHODS

Species identification and antibiotic susceptibilities were tested with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and VITEK 2 systems. The clinical data were collected from medical records. Carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates were investigated by antimicrobial susceptibility testing, carbapenemase genes and multilocus sequence typing.

RESULTS

Six kinds of resistant genes and 23 STs were detected. BlaNDM-1 (n=83, 55.3%) was the predominant carbapenemase gene, followed by blaKPC-2 (n=45, 30.0%), blaNDM-5 (n=7, 4.7%), blaIMP-38 (n=6, 4.0%). BlaNDM-1 was predominant in 2017 and 2018, whereas blaKPC-2 increased in 2019 and became the predominant gene from 2020 to 2021. ST11 accounted for most infections (n=35, 23.3%), followed by ST278 (n=23, 15.3%), ST17 (n=17, 11. 3%) and ST2735 (n=16, 10.7%). ST278 and ST17 were predominant in 2017 and 2018, whereas ST11 increased in 2019 and became the predominant sequence type from 2020 to 2021. Compared with blaNDM-1, the CRKP strains producing blaKPC-2 were characterized by high resistance to gentamicin, amikacin and levofloxacin and the change trend of drug resistance rate before and after COVID-19 was consistent with that of blaNDM-1 and blaKPC-2.

CONCLUSIONS

The main sequence type of CRKP infection changed dynamically from ST278-NDM-1 to ST11-KPC-2 during the years 2017-2021 in the newborns. Antibiotic exposure and the prevalence of COVID-19 since 2020 may have led to changes in hospital population and lead to the changes.

Prevalence of carbapenem-resistant and extended-spectrum beta-lactamase-producing Enterobacteriaceae in a teaching hospital in Ghana

BACKGROUND

Carbapenem-resistant Enterobacteriaceae (CRE) and Extended-spectrum beta-lactamase (ESBL) production among Gram-negative Enterobacteriaceae is an increasing global challenge due to the high morbidity and mortality associated with their infections, especially in developing countries where there are little antibiotic treatment options. Despite these challenges, few studies in Ghana have described the burden of CRE. Therefore, this study aimed to determine the prevalence of carbapenem-resistant Enterobacteriaceae isolated from patients at the Cape Coast Teaching Hospital (CCTH) in the Central region of Ghana.

METHODOLOGY/PRINCIPAL FINDINGS

Enterobacteriaceae isolates were collected from April to July 2019 at the bacteriology unit of CCTH using a consecutive sampling method. Isolates were identified by standard microbiological techniques and confirmed using API 20E. Kirby Bauer disc diffusion method was used to determine the antibiogram of isolates. Isolates were also subjected to ESBL testing using the single-disc combination method. Carbapenem-resistant isolates were identified by the Kirby Bauer disc diffusion method and then examined genotypically for the presence of blaKPC-1, blaIMP-1, blaVIM-1, blaNDM-1, and blaOXA-48 genes via polymerase chain reaction (PCR). Of the 230 isolates comprising E. coli (40.9%), Citrobacter spp. (32.6%), K. pneumoniae (9.1%), P. mirabilis (6.1%), P. vulgaris (5.2%), Enterobacter spp (3.5%)., K. oxytoca (2.2%), and Serratia marcenses (0.4%). Most isolates were from urine 162(70.4%) and wound samples. The isolates showed high resistance to ampicillin 171 (74.3%) and cefuroxime 134(58.3%). The prevalence of MDR was 35.2% (81), with E. coli 40(42.6%) being the majority that exhibited MDR. Of the 230 isolates, 113(49.1%) were ESBL producers, with E. coli 54(57.5%) accounting for the majority, while Serratia marcenses was the least. Of the 13 (5.7%) CRE isolates that showed resistance towards carbapenem in the disc diffusion method, 11 showed the presence of the blaNDM-1 gene, while all isolates showed the presence of the blaOXA-48 gene.

CONCLUSION

The prevalence of carbapenem resistance and ESBL-producing Enterobacteriaceae pathogens among patients at the Cape Coast Teaching Hospital is high and alarming. Therefore, it is imperative to consider effective infection prevention and control measures should be implemented at the hospital to prevent the rapid spread of these dangerous organisms.

Characterization and fitness cost analysis of two plasmids carrying different subtypes of blaNDM in aquaculture farming

In recent years, the blaNDM gene, which mediate resistance to carbapenems, has disseminated all over the world, and has also been detected in animals. Understanding the dissemination and accumulation of antibiotic resistance genes (ARGs) in a human-impacted environment is essential to solve the food safety problems caused by antibiotics. In this study, two strains of carbapenem bacteria carrying blaNDM were screened from 244 strains isolated from two T. sinensis farms in Zhejiang province, China. After their plasmids were isolated and sequenced, their structure and gene environment were analyzed and the mechanism of blaNDM gene transfer was explored. The study measured the fitness cost of plasmids carrying different blaNDM subtypes by four biological characteristics experiments. The results showed that the fitness cost of IncC plasmid carrying blaNDM-1 was higher than that of IncX3 plasmid carrying blaNDM-5. Furthermore, the real-time PCR showed that the decrease of transcription level of fitness-related genes lead to the different fitness cost of plasmids carrying different blaNDM subtypes. Fitness of many blaNDM-harboring plasmids enhanced the further dissemination of this gene and increase the risk of blaNDM gene spreading in aquatic environment, and thus further investigation of carbapenem-resistant bacterias among food animals are in urgent need.

An overview of carbapenem-resistant organisms from food-producing animals, seafood, aquaculture, companion animals, and wildlife

Carbapenem resistance (CR) is a major global health concern. CR is a growing challenge in clinical settings due to its rapid dissemination and low treatment options. The characterization of its molecular mechanisms and epidemiology are highly studied. Nevertheless, little is known about the spread of CR in food-producing animals, seafood, aquaculture, wildlife, their environment, or the health risks associated with CR in humans. In this review, we discuss the detection of carbapenem-resistant organisms and their mechanisms of action in pigs, cattle, poultry, seafood products, companion animals, and wildlife. We also pointed out the One Health approach as a strategy to attempt the emergency and dispersion of carbapenem-resistance in this sector and to determine the role of carbapenem-producing bacteria in animals among human public health risk. A higher occurrence of carbapenem enzymes in poultry and swine has been previously reported. Studies related to poultry have highlighted P. mirabilis, E. coli, and K. pneumoniae as NDM-5- and NDM-1-producing bacteria, which lead to carbapenem resistance. OXA-181, IMP-27, and VIM-1 have also been detected in pigs. Carbapenem resistance is rare in cattle. However, OXA- and NDM-producing bacteria, mainly E. coli and A. baumannii, are cattle's leading causes of carbapenem resistance. A high prevalence of carbapenem enzymes has been reported in wildlife and companion animals, suggesting their role in the cross-species transmission of carbapenem-resistant genes. Antibiotic-resistant organisms in aquatic environments should be considered because they may act as reservoirs for carbapenem-resistant genes. It is urgent to implement the One Health approach worldwide to make an effort to contain the dissemination of carbapenem resistance.

Genomic Epidemiology and Characterization of Carbapenem-Resistant Klebsiella pneumoniae in ICU Inpatients in Henan Province, China: a Multicenter Cross-Sectional Study

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has disseminated globally and is difficult to treat, causing increased morbidity and mortality rates in critically ill patients. We conducted a multicenter cross-sectional study of intensive care unit (ICU) inpatients in 78 hospitals to investigate the prevalence and molecular characteristics of CRKP in Henan Province, China, a hyperepidemic region. A total of 327 isolates were collected and downsampled to 189 for whole-genome sequencing. Molecular typing revealed that sequence type 11 (ST11) of clonal group 258 (CG258) was predominant (88.9%, n = 168), followed by ST2237 (5.8%, n = 11) and ST15 (2.6%, n = 5). We used core genome multilocus sequence typing (cgMLST) to further classified the population into 13 subtypes. Capsule polysaccharide (K-antigen) and lipopolysaccharide (LPS; O-antigen) typing revealed that K64 (48.1%, n = 91) and O2a (49.2%, n = 93) were the most common. We studied isolates collected from both the airway and the gut of the same patients and showed that intestinal carriage was associated with respiratory colonization (odds ratio = 10.80, P < 0.0001). Most isolates (95.2%, n = 180) showed multiple drug resistance (MDR), while 59.8% (n = 113) exhibited extensive drug resistance (XDR), and all isolates harbored either blaKPC-2 (98.9%, n = 187) or blaCTX-M and blaSHV extended-spectrum beta-lactamases (ESBLs) (75.7%, n = 143). However, most were susceptible to ceftazidime-avibactam (CZA) (94.7%, n = 179) and colistin (97.9%, n = 185). We found mgrB truncations in isolates conferring resistance to colistin and mutations in blaSHV and OmpK35 and OmpK36 osmoporins in CZA-resistant isolates. Using a regularized regression model, we found that the aerobactin sequence type and the salmochelin sequence type, among others, were predictors of the hypermucoviscosity phenotype. IMPORTANCE In this study, we address the ongoing epidemic of carbapenem-resistant Klebsiella pneumoniae, a critical threat to public health. The alarming genotypic and phenotypic convergence of multidrug resistance and virulence highlights the increasingly aggravated threat posed by K. pneumoniae. This calls for a combined effort of physicians and scientists to study the potential mechanisms and establish guidelines for antimicrobial therapies and interventions. To this end, we have conducted a genomic epidemiology and characterization study using isolates collected in a coordinated effort of multiple hospitals. Innovative biological discoveries of clinical importance are made and brought to the attention of clinical researchers and practitioners. This study presents an important advance in the application of genomics and statistics to recognize, understand, and control an infectious disease of concern.

Molecular characteristics and virulence factors of carbapenem-resistant Klebsiella pneumoniae among pediatric patients in Shanghai, China

We retrospectively investigated CRKP isolates among 92 pediatric patients (32 neonates and 60 non‑neonates) in 2019 and 2020 (59 and 33 isolates, respectively) to investigate the molecular characteristics and virulence factors of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolated from pediatric patients,. All the CRKP isolates were subjected to antimicrobial susceptibility testing, string testing, molecular typing of virulence and carbapenemase genes, and multilocus sequence typing. Hypervirulent K. pneumoniae (Hvkp) was defined based on the detection of the regulator of mucoid phenotype A (rmpA).Sequence type 11 (ST11) accounted for the majority of infections in both neonates (37.5%) and non‑neonates (43.3%) (P > 0.05), whereas it increased from 30.5% (18/59) in 2019 to 60.6% (20/33) in 2020 (P < 0.05). Carbapenemase gene KPC-2 was predominant in both neonates and non‑neonates (46.9% vs. 51.7%, respectively), followed by New Delhi metallo-beta-lactamase 1 (NDM-1) (34.4% vs. 28.3%, respectively) (all P > 0.05). Compared to 2019, the proportion of bla_NDM-1 decreased (44.1% vs. 6.1%) (P < 0.001), while that of bla_KPC-2 increased (40.7% vs. 66.7%) (P = 0.017) in 2020. ybtS and iutA had a higher positivity rate in KPC-2 and ST11 producers (all P < 0.05); the KPC-2-, ybtS-, and iutA-positive isolates showed relatively higher resistance to fluoroquinolones and aminoglycosides, nitrofurantoin, and piperacillin/tazobactam, respectively. Furthermore, the combined expression (95.7%, 88/92) of carbapenemase and virulence-associated genes was detected, with the carbapenemase genes bla_KPC-2 and bla_TEM-1 combined with virulence-associated genes entB, mrkD, and ybtS accounting for the highest percentage (20.7%).Carbapenemase gene mutations in the CRKP strain from 2019 to 2020 highlight the importance of dynamic monitoring. The spread of hypervirulence-associated genes in CRKP strains and the high positivity rates of ybtS and iutA in KPC-2- and ST11-producing ones signify their high virulence potential in pediatric patients.

Molecular characteristics of carbapenem-resistant gram-negative bacilli in pediatric patients in China

BACKGROUND

Carbapenem-resistant gram-negative bacilli (CR-GNB) have been increasingly reported in China. However, dynamic monitoring data on molecular epidemiology of CR-GNB are limited in pediatric patients.

RESULTS

300 CR-GNB isolates (200 Carbapenem-resistant K. pneumoniae (CRKP), 50 carbapenem-resistant A.baumannii (CRAB) and 50 carbapenem-resistant P. aeruginosa (CRPA)) were investigated. The predominant carbapenemase gene was blaNDM-1 (73%) and blaKPC-2 (65%) in neonates and non-neonates. Meanwhile, the predominant STs were ST11 (54%) in neonates and ST17 (27.0%) and ST278 (20.0%) in non-neonates. Notably, a shift in the dominant sequence type of CRKP infections from ST17 /ST278-NDM-1 to ST11-KPC-2 was observed during the years 2017-2021 and KPC-KP showed relatively higher resistance to aminoglycosides and quinolones than NDM-KP.BlaOXA-23 was isolated from all the CRAB isolates while only one isolate expressing blaBIC and 2 isolates expressing blaVIM-2 were found in CRPA isolates. ST195 (22.0%) and ST244 (24.0%) were the most common in CRAB and CRPA isolates and all the STs of CRAB belonged to CC92 while CRPA presents ST types with diversity distribution.

CONCLUSION

CRKP showed different molecular phenotypes in neonates and non-neonates and was changing dynamically and high-risk clone of ST11 KPC-KP should be paid more attention. Most CRKP and CRAB strains shared the same CCs, suggesting that intrahospital transmission may occur, and large-scale screening and more effective measures are urgently needed.

Characterisation of OXA-48-like carbapenemases in Escherichia coli and Klebsiella pneumoniae from North India

The oxacillinase-48 (OXA-48)-like carbapenemases are class D β-lactamases and increasingly reported in Enterobacterial species. The detection of these carbapenemases is challenging and little information is available on the epidemiology and plasmid characteristics of OXA-48-like carbapenemase producers. We detected the presence of OXA-48-like carbapenemases in 500 clinical isolates of Escherichia coli and Klebsiella pneumoniae, followed by detection of other carbapenemases, extended spectrum β-lactamases (ESBLs) and 16S rRNA methyltransferases in OXA-48 producers. Clonal relatedness was studied using pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Finally, plasmid characterisation was performed through conjugation experiment, S1-PFGE and Southern hybridisation. Around 40% of E. coli and K. pneumoniae isolates harboured OXA-48-like β-lactamases. Two OXA-48 allele variants, OXA-232 and OXA-181 were detected in our study. OXA-48 producers co-harbored diverse drug-resistant genes belonging to other classes of carbapenemases, ESBLs and 16S rRNA methyltransferases. OXA-48-like carbapenemase producers exhibited high clonal diversity. Bla OXA-48 carrying plasmids were conjugative, untypable and their size was ~ 45 kb and ~ 104.5 kb in E. coli and K. pneumoniae respectively. In conclusion, OXA-48-like carbapenemases have emerged as major cause of carbapenem resistance in Enterobacteriaceae and probably still being under reported. Strict surveillance and adequate detection methods are needed to prevent the dissemination of OXA-48-like carbapenemases.

Outbreak of colistin resistant, carbapenemase (bla NDM, bla OXA-232) producing Klebsiella pneumoniae causing blood stream infection among neonates at a tertiary care hospital in India

Infections caused by multi-drug resistant Klebsiella pneumoniae are a leading cause of mortality and morbidity among hospitalized patients. In neonatal intensive care units (NICU), blood stream infections by K. pneumoniae are one of the most common nosocomial infections leading to poor clinical outcomes and prolonged hospital stays. Here, we describe an outbreak of multi-drug resistant K. pneumoniae among neonates admitted at the NICU of a large tertiary care hospital in India. The outbreak involved 5 out of 7 neonates admitted in the NICU. The antibiotic sensitivity profiles revealed that all K. pneumoniae isolates were multi-drug resistant including carbapenems and colistin. The isolates belonged to three different sequence types namely, ST-11, ST-16 and ST-101. The isolates harboured carbapenemase genes, mainly bla _NDM-1, bla _NDM-5 and bla _OXA-232 besides extended-spectrum β-lactamases however the colistin resistance gene mcr-1, mcr-2 and mcr-3 could not be detected. Extensive environmental screening of the ward and healthcare personnel led to the isolation of K. pneumoniae ST101 from filtered incubator water, harboring bla _NDM-5, bla _OXA-232 and ESBL genes (bla _CTX-M) but was negative for the mcr genes. Strict infection control measures were applied and the outbreak was contained. This study emphasizes that early detection of such high-risk clones of multi-drug resistant isolates, surveillance and proper infection control practices are crucial to prevent outbreaks and further spread into the community.

Risk factors and molecular epidemiology of fecal carriage of carbapenem resistant Enterobacteriaceae in patients with liver disease

BACKGROUND

Carbapenem resistant Enterobacteriaceae (CRE) colonization is a risk factor for CRE infection. CRE infection results in an increase in mortality in patients with cirrhosis. However, minimal data regarding the prevalence and the risk factors of CRE colonization in patients with liver disease yet without liver transplantation are available. The present study aimed to investigate the prevalence, risk factors and molecular epidemiology characteristics of CRE fecal carriage among patients with liver disease.

METHODS

Stool specimens from 574 adult inpatients with liver disease were collected from December 2020 to April 2021. CRE were screened using selective chromogenic agar medium and identified by the Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Antimicrobial susceptibility was determined using the broth microdilution method. Carbapenemase genes were characterized by polymerase chain reaction (PCR) and DNA sequencing. Multilocus sequence typing (MLST) was performed for Carbapenem Resistant Klebsiella pneumoniae (CR-KPN) isolates and Carbapenem Resistant Escherichia Coli (CR-ECO) isolates.

RESULTS

The total number of stool specimens (732) were collected from 574 patients with liver disease. 43 non-duplicated CRE strains were isolated from 39 patients with a carriage rate of 6.79% (39/574). The carriage rate was 15.60% (17/109) in patients with acute-on-chronic liver failure (ACLF). Multivariate analysis indicated that ACLF (P = 0.018), the history of pulmonary infection within past 3 months (P = 0.001) and the use of third generation cephalosporin/β-lactamases inhibitor within past 3 months (P = 0.000) were independent risk factors of CRE colonization in patients with liver disease. Klebsiella Pnuemoniae (KPN) (51.28%) and Escherichia coli (ECO) (30.77%) were main strains in these patients. All CRE strains showed high resistance to most antimicrobials except for polymyxin B and tigecycline. Most (83.72%, 36/43) of the CRE carried carbapenemase genes. bla_KPC-2 was the major carbapenemase gene. The molecular epidemiology of KPN were dominated by ST11, while the STs of ECO were scattered.

CONCLUSIONS

The present study revealed that CRE fecal carriage rates were higher in patients with ACLF than in patients without liver failure. ACLF, the history of pulmonary infection within past 3 months and the use of third generation cephalosporin/β-lactamases inhibitor within past 3 months were independent risk factors of CRE colonization in patients with liver disease. Regular CRE screening for hospitalized patients with liver disease should be conducted to limit the spread of CRE strain.

Genomic Characterization of an Extensively Drug-Resistant Extra-Intestinal Pathogenic (ExPEC) Escherichia coli Clinical Isolate Co-Producing Two Carbapenemases and a 16S rRNA Methylase

An extensively drug-resistant Escherichia coli clinical isolate (N1606) belonging to Sequence Type 361 was recovered from the urine of a patient hospitalized in Switzerland. The strain showed resistance to virtually all β-lactams including the latest generation antibiotics cefiderocol and aztreonam-avibactam. Whole genome sequencing revealed that it possessed two carbapenemase-encoding genes, namely bla_NDM-5 and bla_KPC-3, and a series of additional β-lactamase genes, including bla_CTX-M-15 and bla_SHV-11 encoding extended-spectrum β-lactamases (ESBLs), bla_CMY-145 encoding an AmpC-type cephalosporinase, and bla_OXA-1 encoding a narrow-spectrum class D ß-lactamase. Most of these resistance genes were located on plasmids (IncFII-FIA, IncX3, IncIγ, IncFII). That strain exhibited also a four amino-acid insertion in its penicillin-binding protein 3 (PBP3) sequence, namely corresponding to YRIN. Complete genome analysis revealed that this E. coli isolate carried virulence factors (sitA, gad, hra, terC, traT, and cia) and many other non-β-lactam resistance determinants including rmtB, tet(A), dfrA17 (two copies), aadA1, aadA5 (two copies), sul1 (two copies), qacE (two copies), qepA, mdf(A), catA1, erm(B), mph(A), and qnrS1, being susceptible only to tigecycline, colistin and fosfomycin. In conclusion, we described here the phenotypic and genome characteristics of an extensively drug-resistant (XDR) E. coli ST361 being recognized as an emerging clone worldwide.

Emergence of a novel hybrid mcr-1-bearing plasmid in an NDM-7-producing ST167 Escherichia coli strain of clinical origin

Colistin is considered as an antibiotic of ‘last resort’ for the treatment of lethal infections caused by carbapenem-resistant Enterobacterales (CRE), dissemination of plasmid-borne colistin resistance gene mcr-1, particularly into CRE, resulting in the emergence of strains that approach pan-resistance. A wide variety of plasmid types have been reported for carrying mcr-1. Among which, large IncHI2-type plasmids were multidrug-resistant (MDR) plasmids harbored multiple resistance determinants in addition to mcr-1. Herein, we characterized a novel hybrid IncHI2-like mcr-1-bearing plasmid in an NDM-7-producing ST167 Escherichia coli strain EC15-50 of clinical origin. Antimicrobial susceptibility testing showed E. coli EC15-50 exhibited an extensively drug-resistant (XDR) profile that only susceptible to amikacin and tigecycline. S1-PFGE, Southern hybridization and Whole-genome Sequencing (WGS) analysis identified a 46,161 bp blaNDM-7-harboring IncX3 plasmid pEC50-NDM7 and a 350,179 bp mcr-1-bearing IncHI2/HI2A/N/FII/FIA plasmid pEC15-MCR-50 in E. coli EC15-50. Sequence detail analysis revealed the type IV coupling protein (T4CP) gene was absent on pEC15-MCR-50, explaining that pEC15-MCR-50 was a non-conjugative plasmid. Comparative genetic analysis indicated the hybrid plasmid pEC15-MCR-50 was probably originated from pXGE1mcr-like IncHI2/HI2A/N plasmid and pSJ_94-like IncFII/FIA plasmid, and generated as a result of a replicative transposition process mediated by IS26. Currently, the prevalent mcr-1-carrying IncHI2 plasmids were rarely reported to be fused with other plasmids. The identification of the novel hybrid plasmid pEC15-MCR-50 in this study highlighted the importance of close surveillance for the emergence and dissemination of such fusion MDR plasmids, particularly in NDM-producing Enterobacterales.

Genomic Epidemiology Insights on NDM-Producing Pathogens Revealed the Pivotal Role of Plasmids on blaNDM Transmission

Incidences of nosocomial infections mediated by New Delhi metallo-β-lactamase (NDM) enzyme-producing Enterobacterales are increasing globally, resulting in a great burden to public health. The carbapenem-resistant Enterobacterales (CRE) were collected from Henan, China during 2013-2016. The blaNDM-positive strains were characterized using PCR, antimicrobial susceptibility testing, conjugation assay, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), Southern blot, whole-genome sequencing (WGS), and bioinformatics analysis. Eighty-one NDM-producing strains were identified among 391 nonduplicate CRE strains. Among them, four strains cocarried mcr and blaNDM genes, and two carried blaIMP-4 and blaNDM genes. The coexistence of blaNDM-5 and mcr-9 in Enterobacter hormaechei was found for the first time. In total, four blaNDM subtypes were identified. Among them, blaNDM-1 and blaNDM-5 were predominant. There was an obvious increasing trend in blaNDM-5 from 2013 to 2016. Thirteen different bacterial species were found among the 81 strains, and Escherichia coli was the dominant strain. blaNDM genes were located on nine different Inc-type plasmids, most of them on the IncX3 plasmids, except for the Pr-15-2-50 strain, which was located on the chromosome. We characterized two novel plasmids: the IncHI5-like plasmid carrying blaNDM-9 found in K. pneumonia, and the IncI1 blaNDM-5-positive plasmid. These findings provide the genomic basis for the widespread transmission of blaNDM and pave the way for the formulation of more effective monitoring and control methods. IMPORTANCE To control the emergence and transmission of CRE, it is important to perform retrospective genomic investigations. It is important to evaluate the plasmid diversity, genetic environment, and evolutionary relationships of the blaNDM-positive clinical strains in the early transmission stages. This study conducted an in-depth analysis of blaNDM-positive pathogens during a 4-year period using different methods for observing the high prevalence and active transmission of blaNDM-positive CRE. Moreover, we also explored the coexistence of the blaNDM and mcr, a clinically important mobile colistin resistance gene. This study shows that the prevalence of blaNDM-positive pathogens in Henan is high and the isolation rates increase each year. Moreover, plasmid-mediated horizontal transfer plays an important role in blaNDM dissemination. The co-occurrence of multiple resistance genes highlighted a long-lasting evolutionary pathway. Therefore, we have suggested the long-term continuous surveillance of clinical pathogens carrying blaNDM to learn the future transmission trend and curb the public health risk caused by CRE.

Deciphering the Epidemiological Characteristics and Molecular Features of bla KPC-2- or bla NDM-1-Positive Klebsiella pneumoniae Isolates in a Newly Established Hospital

The emergence of hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) was regarded as an emerging threat in clinical settings. Here, we investigated the prevalence of CRKP strains among inpatients in a new hospital over 1 year since its inception with various techniques, and carried out a WGS-based phylogenetic study to dissect the genomic background of these isolates. The genomes of three representative bla_NDM–1-positive strains and the plasmids of four bla_KPC–2-positive strains were selected for Nanopore long-read sequencing to resolve the complicated MDR structures. Thirty-five CRKP strains were identified from 193 K. pneumoniae isolates, among which 30 strains (85.7%) harbored bla_KPC–2, whereas the remaining five strains (14.3%) were positive for bla_NDM–1. The antimicrobial resistance profiles of bla_NDM–1-positive isolates were narrower than that of bla_KPC–2-positive isolates. Five isolates including two bla_NDM–1-positive isolates and three bla_KPC–2-positive strains could successfully transfer the carbapenem resistance phenotype by conjugation. All CRKP strains were categorized into six known multilocus sequence types, with ST11 being the most prevalent type. Phylogenetic analysis demonstrated that the clonal spread of ST11 bla_KPC–2-positive isolates and local polyclonal spread of bla_NDM–1-positive isolates have existed in the hospital. The bla_NDM–1 gene was located on IncX3, IncFIB/IncHI1B, and IncHI5-like plasmids, of which IncFIB/IncHI1B plasmid has a novel structure. By contrast, all ST11 isolates shared the similar bla_KPC–2-bearing plasmid backbone, and 11 of them possessed pLVPK-like plasmids. In addition, in silico virulome analysis, Galleria mellonella larvae infection assay, and siderophore secretion revealed the hypervirulence potential of most bla_KPC–2-positive strains. Given that these isolates also had remarkable environmental adaptability, targeted measures should be implemented to prevent the grave consequences caused by hv-CRKP strains in nosocomial settings.

Klebsiella oxytoca Complex: Update on Taxonomy, Antimicrobial Resistance, and Virulence

Klebsiella oxytoca is actually a complex of nine species-Klebsiella grimontii, Klebsiella huaxiensis, Klebsiella michiganensis, K. oxytoca, Klebsiella pasteurii, Klebsiella spallanzanii, and three unnamed novel species. Phenotypic tests can assign isolates to the complex, but precise species identification requires genome-based analysis. The K. oxytoca complex is a human commensal but also an opportunistic pathogen causing various infections, such as antibiotic-associated hemorrhagic colitis (AAHC), urinary tract infection, and bacteremia, and has caused outbreaks. Production of the cytotoxins tilivalline and tilimycin lead to AAHC, while many virulence factors seen in Klebsiella pneumoniae, such as capsular polysaccharides and fimbriae, have been found in the complex; however, their association with pathogenicity remains unclear. Among the 5,724 K. oxytoca clinical isolates in the SENTRY surveillance system, the rates of nonsusceptibility to carbapenems, ceftriaxone, ciprofloxacin, colistin, and tigecycline were 1.8%, 12.5%, 7.1%, 0.8%, and 0.1%, respectively. Resistance to carbapenems is increasing alarmingly. In addition to the intrinsic bla_OXY, many genes encoding β-lactamases with varying spectra of hydrolysis, including extended-spectrum β-lactamases, such as a few CTX-M variants and several TEM and SHV variants, have been found. bla_KPC-2 is the most common carbapenemase gene found in the complex and is mainly seen on IncN or IncF plasmids. Due to the ability to acquire antimicrobial resistance and the carriage of multiple virulence genes, the K. oxytoca complex has the potential to become a major threat to human health.

Carbapenem-resistant Enterobacterales colonization and subsequent infection in a neonatal intensive care unit in Shanghai, China

Background

Colonization has been reported to play an important role in carbapenem-resistant Enterobacterales (CRE) infection; however, the extent to which carriers develop clinical CRE infection and related risk factors in neonatal intensive care unit (NICU) patients is unclear.

Aim

To investigate the frequency of CRE colonization and its contribution to infections in NICU patients.

Methods

CRE colonization screening and CRE infection surveillance were performed in the NICU in 2017 and 2018.

Findings

Among 1230 unique NICU patients who were screened for CRE colonization, 144 patients tested positive (11.7%, 144/1230), with 9.2% (110/1197) in the intestinal tract, which was higher than that in the upper respiratory tract (6.6%, 62/945) (P=0.026). Gestational age, low birth weight and prolonged hospitalization were risk factors for CRE colonization (all P<0.001). Diversilab homology monitoring found an overall 17.4% (25/144) risk of infection among patients colonized with CRE. For carbapenem-resistant Klebsiella pneumoniae (CR-KP) and carbapenem-resistant Escherichia coli (CR-ECO), the risks were 19.1% (21/110) and 13.8% (4/29), respectively. The independent risk factors for CR-KP clinical infection among CR-KP carriers were receiving mechanical ventilation (odds ratio (OR), 10.177; 95% confidence interval (CI), 2.667–38.830; P=0.013), a high level of neonatal nutritional risk assessment (OR, 0.251; 95% CI, 0.072–0.881; P=0.031) and a high neonatal acute physiology II (SNAP-II) score (OR, 0.256; 95% CI, 0.882–1.034; P=0.025).

Conclusions

The colonization of CRE may increase the incidence of corresponding CRE infection in NICU patients. Receiving mechanical ventilation, malnutrition and critical conditions with high SNAP-II scores were independent risk factors for subsequent CR-KP clinical infection.

Genetic Characterisation of Colistin Resistant Klebsiella pneumoniae Clinical Isolates From North India

Background

Increasing use of colistin has led to the world-wide emergence of mobile colistin resistant gene (mcr). The present study aimed to identify and characterise mcr and other drug-resistant genes in colistin resistant Klebsiella pneumoniae clinical isolates.

Methods

Twenty-two colistin resistant K. pneumoniae were analysed for mcr and other drug-resistant genes, efflux pumps, and virulence genes, and for their biofilm forming ability. Pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) were performed for all mcr-1 positive isolates. S1-PFGE and Southern hybridisation were performed for localisation of mcr-1 and bla_NDM.

Results

Nineteen colistin resistant K. pneumoniae harboured mcr-1 and 3 had mgrB disruption. All isolates harboured bla_OXA-48-type and ESBL genes; eight strains (five with mcr-1 and three with mgrB disruption) co-harboured bla_NDM. Efflux pumps genes AcrAB and mdtK were detected in all 22 and tol-C in 21 isolates. Virulence-related genes entB and irp-1 were detected in all 22, mrkD in 20, and fimH-1 in 18 isolates; 11 isolates were strong biofilm producers. PFGE clustered mcr-1 positive isolates into eight groups based on ≥90% similarity; MLST revealed diverse sequence types, predominant being ST-15 (n = 4) and ST-16 (n = 4). Both mcr-1 and bla_NDM were localised on plasmid and chromosome; mcr-1 was present on IncFII type and bla_NDM on IncFIB and IncA/C type plasmids.

Conclusions

Colistin resistance in K. pneumoniae was predominantly mediated by mcr-1. Co-existence of colistin, carbapenem, and other drug-resistant genes along with efflux pumps indicates towards enormous genomic plasticity in K. pneumoniae with ability to emerge as super-spreader of drug-resistance.

Molecular Characterization of bla IMP - 4 -Carrying Enterobacterales in Henan Province of China

Carbapenem-resistant Enterobacterales (CRE) pose a serious threat to clinical management and public health. We investigated the molecular characteristics of 12 IMP-4 metallo-β-lactamase-producing strains, namely, 5 Enterobacter cloacae, 3 Escherichia coli, 2 Klebsiella pneumoniae, and 2 Citrobacter freundii. These strains were collected from a tertiary teaching hospital in Zhengzhou from 2013 to 2015. The minimum inhibitory concentration (MIC) results showed that each bla_IMP–4-positive isolate was multidrug-resistant (MDR) but susceptible to colistin. All of the E. coli belonged to ST167, two C. freundii isolates belonged to ST396, and diverse ST types were identified in E. cloacae and K. pneumoniae. S1-PFGE, Southern blotting, and PCR-based replicon typing assays showed that the bla_IMP–4-carrying plasmids ranged from ∼52 to ∼360 kb and belonged to FII, FIB, HI2/HI2A, and N types. N plasmids were the predominant type (8/12, 66.7%). Plasmid stability testing indicated that the bla_IMP–4-carrying N-type plasmid is more stable than the other types of plasmids. Conjugative assays revealed that three of the bla_IMP–4-carrying N plasmids were transferrable. Complete sequence analysis of a representative N type (pIMP-ECL14–57) revealed that it was nearly identical to pIMP-FJ1503 (KU051710) (99% nucleotide identity and query coverage), an N-type bla_IMP–4-carrying epidemic plasmid in a C. freundii strain. PCR mapping indicated that a transposon-like structure [IS6100-mobC-intron (K1.pn.I3)-bla_IMP–4-IntI1-IS26] was highly conserved in all of the N plasmids. IS26 involved recombination events that resulted in variable structures of this transposon-like module in FII and FIB plasmids. The bla_IMP–4 gene was captured by a sul1-type integron In1589 on HI2/HI2A plasmid pIMP-ECL-13–46.

Molecular characterization of carbapenem-resistant Enterobacteriaceae and emergence of tigecycline non-susceptible strains in the Henan province in China: a multicentrer study

Introduction

Carbapenem-resistant Enterobacteriaceae (CRE) have been responsible for nosocomial outbreaks worldwide and have become endemic in several countries.

Hypothesis/Gap Statement

To better understand the epidemiological trends and characteristics of CRE in the Henan province.

Aim

We assessed the molecular epidemiological characteristics of 305 CRE strains isolated from patients in 19 secondary or tertiary hospitals in ten areas of the Henan province in China.

Methodology

A total of 305 CRE isolates were subjected to multiple tests, including in vitro antimicrobial susceptibility testing, PCR for carbapenemase genes bla_KPC, bla_NDM, bla_IMP, bla_VIM, bla_OXA-_48-like. Tigecycline-resistant genes ramR, oqxR, acrR, tetA, rpsJ, tetX, tetM, tetL were analysed in five tigecycline non-susceptible carbapenem-resistant Klebsiella pneumoniae isolates (TNSCRKP). Additionally, multilocus sequence typing (MLST) was performed for carbapenem-resistant K. pneumoniae (CRKP).

Results

The most common CRE species were K. pneumoniae (234, 77 %), Escherichia coli (36, 12 %) and Enterobacter cloacae (13, 4 %). All strains exhibited multi-drug resistance. Overall, 97 % (295/305) and 97 % (297/305) of the isolates were susceptible to polymyxin B and tigecycline, respectively. A total of 89 % (271/305) of the CRE isolates were carbapenemase gene-positive, including 70 % bla_KPC, 13 % bla_NDM, 6 % bla_IMP, and 1 % combined bla_KPC/bla_NDM genes. K. pneumoniae carbapenemase (KPC) was the predominant carbapenemase in K. pneumoniae (87 %), whereas NDM and IMP were frequent in E. coli (53 %) and E. cloacae (69 %), respectively. Mutations in the ramR, tetA, and rpsJ genes were detected in five TNSCRKP. Moreover, 15 unique sequence types were detected, with ST11 (74 %), ST15 (9 %) and ST2237 (5 %) being dominant among K. pneumoniae strains.

Conclusion

A high proportion of CRE strains were carbapenemase-positive, and five carbapenem-resistant K. pneumonia isolates were tigecycline non-susceptible, indicating a need for the ongoing surveillance of CRE and effective measures for the prevention of CRE infections.

Co-infections of two carbapenemase-producing Enterobacter hormaechei clinical strains isolated from the same diabetes individual in China

Introduction. Since mcr-1 was first reported in China, there have been ten variants of MCR appearing nationwide so far. Multidrug-resistant Enterobacteriaceae bacteria carrying both NDM and MCR have become a serious threat to global public health.Hypothesis/Gap Statement. The genetic structure of mcr-9 needs to be better understood in order to better prevent and control the transmission of drug-resistant genes.Aims. The aim of this study was to characterize the presence of two Enterobacter hormaechei isolates, which carries bla _NDM-5 CME2 and the coexistence of mcr-9 and bla _NDM-1 strain CMD2, which were isolated from a patient with diabetes in Sichuan, China.Methodology. The microbroth dilution method was used for antibiotic susceptibility. Conjugation experiment was used to investigate the transferability of bla _NDM-1, bla _NDM-5 and mcr-9. Whole-genome sequencing was performed on Illumina HiSeq platform. The ability of biofilm formation was detected by crystal-violet staining, the virulence of the bacteria was measured by Galleria mellonella killing assay.Results. bla _NDM-5 carrier CME2 and CMD2 with bla _NDM-1 and mcr-9 were resistant to carbapenems, β-lactam, aminoglycoside, quinolone and tetracycline, while CMD2 was also resistant to colistin. Conjugation assay and plasmid replicon typing further demonstrated that both bla _NDM-1 and bla _NDM-5 were respectively present on the self-transferrable IncX3 plasmid, mcr-9 was located on the self-transferrable IncHI2 plasmid. Through the analysis of mcr-9 gene context, the structure was DUF4942-rcnR-rcnA-copS-IS903-mcr-9-wbuC-qseC-qseB-IS1R-ΔsilR-IS903, bla _NDM-1 context was IS3000-ΔISAba125-IS5-bla _NDM-1-ble-trpF-groS-groL-insE-ΔIS26 structure, bla _NDM-5 structure was IS3000-bla _NDM-5-ble-trpF-dsbC-ΔIS26-umuD-ISKox3-tnpR-parA. Biofilm formation of CME2 was stronger than CMD2. There was no significant difference in virulence between the two strains.Conclusion. This study reveals two multiple drug-resistant E. hormaechei isolates from diabetes patient samples. E. hormaechei carrying two NDM-resistant genes is already a serious threat, where MCR is an important cause of treatment failure in bacterial infections. This study is a reminder not only to prevent infection in patients with diabetes, but also to constantly monitor the epidemic and spread of the drug-resistant gene.

Molecular Characterization of an IncFIIk Plasmid Co-harboring bla IMP-26 and tet(A) Variant in a Clinical Klebsiella pneumoniae Isolate

Carbapenems and tigecycline are two important classes of antimicrobial agents to treat the infections caused by Enterobacterales. Here, we reported a plasmid carrying both bla_IMP–26 and tet(A) variant in clinical Klebsiella pneumoniae KP-1572. MIC results showed that K. pneumonia KP-1572 was resistant to a wide range of antimicrobials. The bla_IMP–26 and tet(A) variant were located on an identical plasmid, which was indicated by S1-PFGE and southern blotting hybridization and can be successfully transferred by electroporation. Whole-plasmid sequencing and analysis revealed that a 142,993-bp-sized plasmid, designated pIMP1572, contains an IncFII_k backbone and a variable region harboring bla_IMP–26 and tet(A) variant. The plasmid pIMP1572 was apparently originated from a tet(A)-carrying IncFII_k plasmid but with a deletion length of 6,216-bp and a multiple drug resistance region (MDRR) insertion of 25,259 bp. The plasmid pIMP1572 in the present study represents the first report of the IncFII_k plasmid co-carrying bla_IMP and tet(A) variant, which should be monitored.

Genomic Features and Virulence Characteristics of a Community-Acquired Bloodstream Infection-Causing Hypervirulent Klebsiella pneumoniae ST86 Strain Harboring KPC-2-Encoding IncX6 Plasmid

The emergence and spread of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) is causing worldwide concern. Sequence type (ST) 86 K. pneumoniae, a major hvKP clone, is rarely resistant to carbapenem. In this study, we report the genomic features and virulence characteristics of a community-acquired bloodstream infection (CA-BSI)-causing CR-hvKP ST86 strain (KPN55602). This strain is resistant to carbapenem but sensitive to amikacin, gentamicin, tigecycline, and colistin. According to in vitro and in vivo virulence assessments, it was classified as hypervirulent. Whole-genome sequencing revealed that KPN55602 has a single 5.13 Mb chromosome and two plasmids. The chromosome of KPN55602 is phylogenetically similar to those of other sequenced ST86 strains. The incompatibility (Inc) group HI1B plasmid pK55602_1, harboring a set of virulence genes, was classified as a virulence plasmid. The IncX6 plasmid pK55602_2, carrying bla_KPC-2, was transferable through conjugation and is highly homologous to all five sequenced bla_KPC-bearing IncX6 plasmids. In conclusion, to our knowledge, this is the first report of a CA-BSI-causing CR-hvKP ST86 strain harboring an exogenous bla_KPC-2-bearing IncX6 plasmid, supplementing existing knowledge on the CR-hvKP evolutionary scenario. The IncX6 plasmid may be an important vehicle for bla_KPC, and its horizontal transfer may have led to CR-hvKP evolution in the community setting.

Molecular Mechanisms, Epidemiology, and Clinical Importance of β-Lactam Resistance in Enterobacteriaceae

Despite being members of gut microbiota, Enterobacteriaceae are associated with many severe infections such as bloodstream infections. The β-lactam drugs have been the cornerstone of antibiotic therapy for such infections. However, the overuse of these antibiotics has contributed to select β-lactam-resistant Enterobacteriaceae isolates, so that β-lactam resistance is nowadays a major concern worldwide. The production of enzymes that inactivate β-lactams, mainly extended-spectrum β-lactamases and carbapenemases, can confer multidrug resistance patterns that seriously compromise therapeutic options. Further, β-lactam resistance may result in increases in the drug toxicity, mortality, and healthcare costs associated with Enterobacteriaceae infections. Here, we summarize the updated evidence about the molecular mechanisms and epidemiology of β-lactamase-mediated β-lactam resistance in Enterobacteriaceae, and their potential impact on clinical outcomes of β-lactam-resistant Enterobacteriaceae infections.

Emergence of Escherichia coli isolates producing NDM-1 carbapenemase from waterfowls in Hainan island, China

Carbapenems are traditionally recognized to be the last resort drugs to treat infections due to MDR organisms such as E. coli. As such, the emergence of New Delhi metallo-β-lactamase-producing E. coli strains have become a challenging threat to the public health. In this regard, we examined the molecular characteristics of carbapenem-resistant E. coli (CRE) isolated from waterfowls in China's tropical island, Hainan. A total of 311 single E. coli strains were obtained from 20 various farms of healthy ducks and geese in 2 districts of Hainan island. The CRE strains were initially identified via phenotypic resistance and modified Hodge test. PCR assay and subsequent nucleotide sequencing were used to detect different types of carbapenemase encoding genes (bla_NDM, bla_VIM, bla_IMP, bla_OXA and bla_KPC). In addition, MLST and PFGE analyses were also performed. Among the 311 E. coli strains, 8 strains were detected to produce a single type of carbapenemase i.e. NDM-1 (2.6%). A total of 5 sequence types (STs) were observed, of which ST10 was the most prevalent accounting for 37.5% (3/8). Moreover, these 8 isolates yielded 6 different PFGE clusters but showed approximately related PFGE types, suggesting the propagation of similar clone between the farms. This is the first report on the identification of NDM-1-producing E. coli from waterfowls in Hainan island, China. Our results emphasize the need for better efforts to control the further spread of NDM-1-producing E. coli strains in this tropical island.

Colonization of Mice With Amoxicillin-Associated Klebsiella variicola Drives Inflammation via Th1 Induction and Treg Inhibition

β-Lactam antibiotics can increase the resistance and virulence of individual intestinal microorganisms, which may affect host physiology and health. Klebsiella, a crucial gut inhabitant, has been confirmed to be resistant to most β-lactam antibiotics and contributes to the etiology of inflammatory bowel disease (IBD). In this study, the influence of amoxicillin (AMO) on Klebsiella and its role in colitis was investigated in an antibiotic cocktail (ABx) murine model. The results suggested that a 7-day AMO treatment significantly enriched the abundance of Klebsiella and enhanced serum resistance, antibiotic resistance, and biofilm formation ability of Klebsiella variicola (K. variicola) compared to the wild-type strain in the control group mice. Colonization of mice with the AMO-associated K. variicola could induce Th1 cells and inhibit Treg differentiation to promote inflammation in ABx murine model. In addition, inoculation of AMO-associated K. variicola in dextran sodium sulfate (DSS)-induced colitis murine model mice also confirmed that K. variicola colonization exacerbated inflammation as assessed by increased TNF-α, IFN-γ, IL-17a, and disease activity (DAI) levels; decreased colon length and bodyweight; and a disrupted Th1/Treg balance. The results of our study demonstrate that AMO enhances Klebsiella virulence in mice by disrupting the T cell equilibrium to exacerbate colitis, thereby providing a reference for proper antibiotic prescription.

Emergence of a novel conjugative hybrid virulence multidrug-resistant plasmid in extensively drug-resistant Klebsiella pneumoniae ST15

INTRODUCTION

Co-existence of both virulence and multidrug-resistant (MDR) determinants on a self-transmissible plasmid facilitates simultaneous transfer of virulence and resistance in a single event and rapid emergence of virulent and MDR Klebsiella pneumoniae clones.

METHOD

This study identified extensively drug-resistant ST15 strains, KP17-15 and KP17-16, from clinical cases with microbiological and genomical approaches.

RESULTS

The chromosomes of KP17-15 and KP17-16 were highly homologous with 12 SNP differences, indicating that the two strains were derived from the same clone. Multiple plasmids existed in the isolates, including novel virulence plasmids p17-15-vir (479 kb) and p17-16-vir (290 kb) for KP17-15 and KP17-16, respectively. Notably, the plasmid p17-15-vir (479 kb) was a hybrid plasmid that might be formed by recombination of two homologous regions encoding group II intron reverse transcriptase and mobile element ISShes11 shared by p17-16-vir (290 kb) and a conjugative MDR plasmid p17-16-CTX (188 kb). p17-15-vir was readily transferable to ST11 Klebsiella pneumoniae by conjugation. Moreover, p17-16-vir, a non-conjugative virulence plasmid lacking the transfer (tra) operon, was also transferable by conjugation under the help of p17-16-CTX or p17-16-KPC. Fusion of p17-16-vir with p17-16-CTX into a p17-15-vir-like plasmid was also observed in the transconjugant.

CONCLUSION

The findings uncover the evolutionary pathway of a novel hybrid virulence MDR plasmid and transfer mechanism of a non-conjugative virulence plasmid. Systematic surveillance of such hybrid virulence MDR plasmids in clinical Klebsiella pneumoniae should be performed.

Actively surveillance and appropriate patients placements' contact isolation dramatically decreased Carbapenem-Resistant Enterobacteriaceae infection and colonization in pediatric patients in China

BACKGROUND

With the increasing use of carbapenems in clinic practice, carbapenem-resistant Enterobacteriaceae (CRE) has also increased, thus posing a significant threat to human health.

AIM

To assess the effects of CRE colonization active screening and various CRE patient placements implemented in decreasing CRE infection risk.

METHODS

CRE colonization screening and various CRE patient placements were performed across CRE high-risk departments (PICU, NICU, neonatal wards and hematology departments) between 2017 and 2018, respectively.

FINDING

In 2018, more than 80% neonatal CRE positive patients were isolated using single room or same room isolation, and more than 50% non-neonatal patients were, with no cohort placement. The CRE nosocomial infection incidences decreased from 1.96% to 0.63% in NICU, and from 0.57% to 0.30% in neonatal wards (all P<0.05) while no significant changes were found in the other departments. The CRE colonization incidence at different length hospital stay (LOS) decreased at 8-14days and >14days LOS in CRE high-risk departments (all P<0.05). In addition, 62.5% clinical strains, 66.7% screening strains, and 74.1% nosocomial infection strains were belonged to CC17 complex group in neonatal isolates; while, 56.6%, 47.5% and 100% strains mentioned above were belonged to CC11 complex group in non-neonatal isolates respectively. The predominant carbapenemase gene was blaNDM-1 (98%) in neonatal and blaKPC-2 (70%) in non-neonatal CR-KP stains.

CONCLUSIONS

Active CRE colonization surveillance and CRE positive patient propriety placement may decrease the CRE infection risk. Neonatal and non-neonatal CR-KP isolates showed different CRE molecular characteristics, which could further benefit CRE infection precaution and antibiotic therapy.

Coexistence of the blaNDM-1-carrying plasmid pWLK-NDM and the blaKPC-2-carrying plasmid pWLK-KPC in a Raoultella ornithinolytica isolate

To date, bla_NDM and bla_KPC genes have been found predominantly in clinical settings around the world. In contrast, bacteria harbouring these two genes from natural environments are relatively less well studied compared to those found in clinical settings. In this study, a carbapenem-resistant Raoultella ornithinolytica strain, WLK218, was isolated from urban river sediment in Zhengzhou City, Henan Province, China. This isolate was subjected to PCR and antimicrobial susceptibility testing. PCR results showed that this isolate was positive for both the bla_NDM-1 and bla_KPC-2 genes. The antimicrobial susceptibility testing results showed that this isolate exhibited resistance or intermediate resistance to all the antibiotics tested except for streptomycin (susceptible) and cefepime (susceptible-dose dependent). The complete genome sequence of the WLK218 isolate was then determined by using a combination of the PacBio and Illumina sequencing technologies. The de novo assembly of the genome generated one chromosome and six plasmids. Among the six plasmids, the bla_NDM-1 gene was carried on the IncX3 plasmid pWLK-NDM, while the bla_KPC-2 gene was located on the untypeable plasmid pWLK-KPC. This is the first report of an environmental Raoultella ornithinolytica isolate co-harbouring the bla_NDM-1 and bla_KPC-2 genes.

Diversity of Virulence Genes in Multidrug Resistant Escherichia coli from a Hospital in Western China

Background

Escherichia coli strains are the most commonly isolated bacteria in hospitals. The normally harmless commensal E. coli can become a highly adapted pathogen, capable of causing various diseases both in healthy and immunocompromised individuals, by acquiring a combination of mobile genetic elements. Our aim was to characterize E. coli strains from a hospital in western China to determine their virulence and antimicrobial resistance potential.

Methods

A total of 97 E. coli clinical isolates were collected from the First Affiliated Hospital of Chengdu Medical College from 2015 to 2016. Microbiological methods, PCR, and antimicrobial susceptibility tests were used in this study.

Results

The frequency of occurrence of the virulence genes fimC, irp2, fimH, fyuA, lpfA, hlyA, sat, and cnf1 in the E. coli isolates was 93.81, 92.78, 91.75, 84.54, 41.24, 32.99, 28.86, and 7.22%, respectively. Ninety-five (97.9%) isolates carried two or more different virulence genes. Of these, 44 (45.4%) isolates simultaneously harbored five virulence genes, 24 (24.7%) isolates harbored four virulence genes, and 17 (17.5%) isolates harbored six virulence genes. In addition, all E. coli isolates were multidrug resistant and had a high degree of antimicrobial resistance.

Conclusion

These results indicate a high frequency of occurrence and heterogeneity of virulence gene profiles among clinical multidrug resistant E. coli isolates. Therefore, appropriate surveillance and control measures are essential to prevent the further spread of these isolates in hospitals.

Multidrug-resistant Acinetobacter baumannii strains with NDM-1: Molecular characterization and in vitro efficacy of meropenem-based combinations

Acinetobacter baumannii is an important cause of hospital-acquired, multidrug-resistant (MDR) infections occurring worldwide. Anti-microbial combination regimens may be the only feasible treatment option for affected patients. In the present study, the efficacy of the combined therapy of meropenem with colistin, ampicillin-sulbactam, tazobactam and vancomycin against clinical strains of MDR A. baumannii was determined. Anti-microbial susceptibility testing was performed and resistance genes were characterized by a multiplex polymerase chain reaction (PCR)-reverse line blot assay. The genetic background of New Delhi metallo-β-lactamase 1 (NDM-1) was analysed by primer walking. The presence of NDM-1 was detected using the modified Hodge test and the EDTA-combined disk test. To screen for synergistic drug effects, the fractional inhibitory concentration index was calculated using a checkerboard assay. The results of the PCR as well as the sequence analyses suggested that NDM-1 was located downstream of the ISAba125 element. In addition, a synergistic effect was determined for meropenem + vancomycin, meropenem + tazobactam and meropenem + ampicillin + sulbactam in two strains each, and in four strains for meropenem + colistin. A total of five A. baumannii strains with resistance to numerous antibiotics and carrying numerous resistance genes were identified. In the strains of A. baumannii, the NDM-1 gene was integrated in a transposon structure with a copy of the ISAba125 insertion sequence. However, the genetic background was not identical among the different species and strains. The genetic variability of NDM-1 may facilitate the rapid dissemination of this gene. In conclusion, meropenem may enhance the efficacy of antibiotics in A. baumannii strains with NDM-1-associated MDR.

Characterization Of bla NDM-5-Positive Escherichia coli Prevalent In A University Hospital In Eastern China

Purpose

The emergence and spread of carbapenem-resistant Enterobacteriaceae deserves special concern worldwide. Unlike the epidemiological characteristics reported in other studies, we found that the production of New Delhi metallo-β-lactamase 5 was the main mechanism for the resistance of Escherichia coli to carbapenems.

Methods

All carbapenem-resistant strains were collected from July 2017 to July 2018 of the First Affiliated Hospital of Nanjing Medical University. The presence of carbapenemase-encoding genes was detected using PCR and gene sequencing. Genetic relatedness of the bla_NDM-5-positive E. coli strains was determined with PFGE and MLST. Susceptibility profiles were measured with broth microdilution method and E-test strips. Transferability features of bla_NDM-5 gene were assessed by conjugation experiments, S1-PFGE, southern blotting and PCR-based replicon typing methods. The genetic structures surrounding bla_NDM-5 were acquired by whole genome sequencing and PCR mapping.

Results

Among the 28 carbapenem-resistant E. coli strains, 18 (64%) were verified as NDM-5 producers. The 18 bla_NDM-5-positive E. coli strains showed high resistance to most antibiotics, but 100% were sensitive to colistin and tigecycline. In addition, the 18 bla_NDM-5-positive E. coli strains belonged to eight STs, among which ST167, ST410 and ST101 were found to cause clonal spread in the hospital. Further studies found that the bla_NDM-5 gene was located on an IncX3-type plasmid, and all plasmids harbored an IS3000-ΔISAba125-IS5-bla_NDM-5-bleMBL-trpF-dsbC-IS26 structure.

Conclusion

The clonal spread of bla_NDM-5-positive E. coli strains and horizontal dissemination via the pNDM-MGR 194-like plasmids should draw more attention. Appropriate infection control operations should be performed to prevent the further spread of bla_NDM-5.

Emergence and transmission of New Delhi metallo-beta-lactamase-5-producing Escherichia coli Sequence Type 361 in a Tertiary Hospital in South Korea

Background

The emergence of carbapenem‐resistant Escherichia coli (E coli) is a serious global health threat, but little is known about carbapenemase‐producing E coli in Daejeon, South Korea. The aim of this study was to investigate characteristics of thirteen carbapenem‐resistant E coli isolates in a tertiary hospital.

Methods

Thirteen non‐duplicate carbapenem‐resistant E coli strains were collected from October 2017 to January 2018. Antimicrobial susceptibility was determined with the E test or disk diffusion method. The carbapenem minimum inhibitory concentrations (MICs) were determined by the agar dilution method. The colistin and tigecycline MICs were determined by broth microdilution. The resistance genes, including carbapenemase genes, were evaluated by polymerase chain reaction, and DNA sequencing was performed to characterize the genes. Pulsed‐field gel electrophoresis and multilocus sequence typing (MLST) were performed to evaluate the clonal relatedness of isolates. The clinical data of patients were retrospectively reviewed.

Results

All the E coli isolates harbored bla_NDM‐5 gene and were resistant to most of the antimicrobial agents, such as carbapenem, cephalosporins, ciprofloxacin, and chloramphenicol, excluding amikacin and colistin. Other resistant genes, such as bla_TEM‐1, bla_CTX‐M‐15, bla_CMY‐2, aac(6')‐Ib‐cr, and qepA, were detected. The E coli isolates harboring bla_NDM‐5 belonged to ST361 (n = 11), ST12 (n = 1), ST410 (n = 1), and PFGE types A (n = 11), B (n = 1), and C (n = 1).

Conclusions

This study reports on an outbreak of a predominant epidemic clone, the NDM‐5 producing, multidrug‐resistant E coli ST361 isolate. These findings suggest that we should pay attention to infection control measures to limit the spread of NDM‐5‐producing pathogens.

High proportion of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae among extended-spectrum β-lactamase-producers in Nigerian hospitals

OBJECTIVES

Carbapenem-resistant Enterobacterales are a global problem, however little is known about the burden and origin of carbapenem resistance in Africa. The objectives of this study were to determine the proportion of carbapenem-resistant isolates among extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E), to identify the underlying mechanisms of resistance and to assess the population structure of carbapenem-resistant isolates from Nigeria.

METHODS

ESBL-E isolates (n = 175) from infections were collected at four hospitals in Lagos, Nigeria, from July 2016 to January 2018 and were screened for carbapenem resistance using a VITEK®2 automated system. All carbapenem-resistant ESBL-E (CRE) were screened for bla_KPC, bla_CTX-M, bla_CMY-2, bla_NDM, bla_VIM, bla_IMP, bla_OXA-181 and bla_OXA-48 genes. Genotyping of randomly selected isolates was performed by whole-genome sequencing.

RESULTS

The isolates included Escherichia coli (n = 113; 64.6%) and Klebsiella pneumoniae (n = 62; 35.4%). Of the 175 ESBL-E isolates, 48 (27.4%) were resistant to carbapenems (15 E. coli and 33 K. pneumoniae). CRE isolates carried bla_NDM (n = 30; 62.5%), bla_NDM + bla_OXA-181 (n = 10; 20.8%), bla_OXA-181 (n = 2; 4.2%) and bla_NDM + bla_OXA-48 (n = 1; 2.1%); no carbapenemase gene was detected in 5 isolates (10.4%). The isolates showed low diversity and were mainly associated with multilocus sequence typing (MLST) sequence types ST410 for E. coli and ST395 and ST147 for K. pneumoniae.

CONCLUSION

Carbapenem resistance is frequent among ESBL-E in Nigeria and is mainly associated with bla_NDM. Genotyping suggested that the observed clones possibly originated from Southeast Asia.

Plasmid evolution in carbapenemase-producing Enterobacteriaceae: a review

Carbapenem-resistant Enterobacteriaceae (CRE) have been listed by the WHO as high-priority pathogens owing to their high association with mortalities and morbidities. Resistance to multiple β-lactams complicates effective clinical management of CRE infections. Using plasmid typing methods, a wide distribution of plasmid replicon groups has been reported in CREs around the world, including IncF, N, X, A/C, L/M, R, P, H, I, and W. We performed a literature search for English research papers, published between 2013 and 2018, reporting on plasmid-mediated carbapenem resistance. A rise in both carbapenemase types and associated plasmid replicon groups was seen, with China, Canada, and the United States recording a higher increase than other countries. bla_KPC was the most prevalent, except in Angola and the Czech Republic, where OXA-181 (n = 50, 88%) and OXA-48-like (n = 24, 44%) carbapenemases were most prevalent, respectively; bla_KPC-2/3 accounted for 70% (n = 956) of all reported carbapenemases. IncF plasmids were found to be responsible for disseminating different antibiotic resistance genes worldwide, accounting for almost 40% (n = 254) of plasmid-borne carbapenemases. bla_CTX-M , bla_TEM , bla_SHV , bla_OXA-1/9 , qnr, and aac-(6')-lb were mostly detected concurrently with carbapenemases. Most reported plasmids were conjugative but not present in multiple countries or species, suggesting limited interspecies and interboundary transmission of a common plasmid. A major limitation to effective characterization of plasmid evolution was the use of PCR-based instead of whole-plasmid sequencing-based plasmid typing.

Prevalence and molecular epidemiology characteristics of carbapenem-resistant Escherichia coli in Heilongjiang Province, China

Objective

This retrospective study was conducted to determine the prevalence and molecular epidemiology characteristics of carbapenem-resistant Escherichia coli (CRE).

Methods

A total of 593 Escherichia coli (E. coli) isolates were recovered from pigs and urban river from 2009 to 2014 in Heilongjiang Province of China. Forty CRE including 22 strains isolated from fecal samples of pigs and 18 strains isolated from water samples were selected. PCR detection of resistance determinants, multi-locus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and phylogenetic groups were performed to characterize CRE isolates. Conjugation experiments, plasmid stability testing, PCR-based replicon typing (PBRT), and PCR mapping were conducted to analyze bla_NDM-carrying plasmids. In vitro time–growth studies and competition experiments were carried out to assess the fitness impact of NDM carriage.

Results

Five NDM-1-positive E. coli isolates were identified from water samples. Genetic environment analysis revealed that a cluster of genes (ISAba125-bla_NDM-1-ble_MBL-ΔtrpF) was detected in all of the NDM-1-positive isolates. Conjugation assays showed that bla_NDM-1 could be successfully transferred to E. coli J53 from 5 donor strains at frequencies of 4.6×10⁻⁵ to 2.6×10⁻². The plasmids from all transconjugants belonged to different plasmid replicon types including IncA/C (n=2), IncFII (n=1) and IncX3 (n=2). In vitro time–growth studies revealed that bla_NDM-1 did not have a significant impact on cell proliferation. Meanwhile, competition experiments showed that the acquisition of bla_NDM-1 can place an energy burden on the bacterial host and incur fitness cost. However, plasmid stability testing showed that bla_NDM-1-carrying plasmid remained stable in the hosts after seven passages without antimicrobial selection.

Conclusion

The study revealed the early molecular epidemiology and dissemination characteristics of CRE. In addition, the overall antimicrobial resistance in E. coli recovered from water samples is higher than the strains isolated from fecal samples of pigs. Furthermore, we isolated and identified five NDM-1-producing E. coli strains from water samples.

Carbapenemase-producing bacteria in food-producing animals, wildlife and environment: A challenge for human health

Antimicrobial resistance is an increasing global health problem and one of the major concerns for economic impacts worldwide. Recently, resistance against carbapenems (doripenem, ertapenem, imipenem, meropenem), which are critically important antimicrobials for human cares, poses a great risk all over the world. Carbapenemases are β-lactamases belonging to different Ambler classes (A, B, D) and encoded by both chromosomal and plasmidic genes. They hydrolyze a broad variety of β-lactams, including carbapenems, cephalosporins, penicillins and aztreonam. Despite several studies in human patients and hospital settings have been performed in European countries, the role of livestock animals, wild animals and the terrestrial and aquatic environment in the maintenance and transmission of carbapenemase- producing bacteria has been poorly investigated. The present review focuses on the carbapenemase-producing bacteria detected in pigs, cattle, poultry, fish, mollusks, wild birds and wild mammals in Europe as well as in non-European countries, investigating the genetic mechanisms for their transmission among food-producing animals and wildlife. To shed light on the important role of the environment in the maintenance and genetic exchange of resistance determinants between environmental and pathogenic bacteria, studies on aquatic sources (rivers, lakes, as well as wastewater treatment plants) are described.

In Vitro and In Vivo Activities of β-Lactams in Combination with the Novel β-Lactam Enhancers Zidebactam and WCK 5153 against Multidrug-Resistant Metallo-β-Lactamase-Producing Klebsiella pneumoniae

Zidebactam and WCK 5153 are novel bicyclo-acyl hydrazide (BCH) agents that have previously been shown to act as β-lactam enhancer (BLE) antibiotics in Pseudomonas aeruginosa and Acinetobacter baumannii The objectives of this work were to identify the molecular targets of these BCHs in Klebsiella pneumoniae and to investigate their potential BLE activity for cefepime and aztreonam against metallo-β-lactamase (MBL)-producing strains in vitro and in vivo Penicillin binding protein (PBP) binding profiles were determined by Bocillin FL assay, and 50% inhibitory concentrations (IC₅₀s) were determined using ImageQuant TL software. MICs and kill kinetics for zidebactam, WCK 5153, and cefepime or aztreonam, alone and in combination, were determined against clinical K. pneumoniae isolates producing MBLs VIM-1 or NDM-1 (plus ESBLs and class C β-lactamases) to assess the in vitro enhancer effect of BCH compounds in conjunction with β-lactams. Additionally, murine systemic and thigh infection studies were conducted to evaluate BLE effects in vivo Zidebactam and WCK 5153 showed specific, high PBP2 affinity in K. pneumoniae The MICs of BLEs were >64 μg/ml for all MBL-producing strains. Time-kill studies showed that a combination of these BLEs with either cefepime or aztreonam provided 1 to >3 log₁₀ kill against MBL-producing K. pneumoniae strains. Furthermore, the bactericidal synergy observed for these BLE-β-lactam combinations translated well into in vivo efficacy even in the absence of MBL inhibition by BLEs, a characteristic feature of the β-lactam enhancer mechanism of action. Zidebactam and WCK 5153 are potent PBP2 inhibitors and display in vitro and in vivo BLE effects against multidrug-resistant (MDR) K. pneumoniae clinical isolates producing MBLs.

Characterization of a novel bla NDM-5-harboring IncFII plasmid and an mcr-1-bearing IncI2 plasmid in a single Escherichia coli ST167 clinical isolate

Background and purpose

The spread of the plasmid-mediated, colistin-resistance gene mcr-1 into New Delhi metallo-β-lactamase (NDM)-producing bacterial isolates can cause untreatable infections. In this study, we conducted a molecular characterization of a novel, conjugative, bla_NDM-5-positive IncFII plasmid (pNDM-EC16-50) together with an mcr-1-bearing IncI2 plasmid in a single Escherichia coli ST167 clinical isolate EC16-50.

Methods and results

EC16-50, which belongs to the E. coli strain ST167 and phylogroup A, was identified to co-produce NDM-5 and MCR-1. S1-PFGE and Southern blotting showed that bla_NDM-5 and mcr-1 genes were located oñ95 kb and ~65 kb plasmids, respectively. A conjugation assay revealed that both bla_NDM-5- and mcr-1-bearing plasmids were self-transmissible. Comparative plasmid analysis suggested that bla_NDM-5-harboring F2:A-:B-plasmid might have evolved from the well-reported NDM-carrying pMC-NDM-like plasmid via recombination with a locally emerged pSJ_94 plasmid, whereas the mcr-1-carrying IncI2 plasmid was similar to previously reported mcr-1-bearing plasmids in China.

Conclusion and impact

This study represents the first report of the NDM-5 carrying Inc-FII- but not IncX3-type plasmid in an MCR-1-producing E. coli isolate. More striking was the dissemination of mcr-1 in a successful epidemic NDM-5-producing E. coli clone ST167, which could facilitate the spread of colistin resistance in carbapenemase-producing E. coli isolates.

The role of wildlife (wild birds) in the global transmission of antimicrobial resistance genes

Antimicrobial resistance is an urgent global health challenge in human and veterinary medicine. Wild animals are not directly exposed to clinically relevant antibiotics; however, antibacterial resistance in wild animals has been increasingly reported worldwide in parallel to the situation in human and veterinary medicine. This underlies the complexity of bacterial resistance in wild animals and the possible interspecies transmission between humans, domestic animals, the environment, and wildlife. This review summarizes the current data on expanded-spectrum β-lactamase (ESBL), AmpC β-lactamase, carbapenemase, and colistin resistance genes in Enterobacteriaceae isolates of wildlife origin. The aim of this review is to better understand the important role of wild animals as reservoirs and vectors in the global dissemination of crucial clinical antibacterial resistance. In this regard, continued surveillance is urgently needed worldwide.

Genetic Diversity of Carbapenem-Resistant Enterobacteriaceae (CRE) Clinical Isolates From a Tertiary Hospital in Eastern China

The prevalence of carbapenem-resistant Enterobacteriaceae (CRE) is increasing globally, with different molecular mechanisms described. Here we studied the molecular mechanisms of carbapenem resistance, including clonal and plasmid dissemination, of 67 CRE isolates collected between 2012 and 2016 from a tertiary hospital in Eastern China, an CRE endemic region. Species identification and susceptibility testing were performed using the BD Phoenix Automated Microbiology System. Isolates were characterized by PCR (for carbapenemases, ESBLs, AmpC and porin genes), multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and conjugation transfer experiments. Selected bla_KPC-2 -harboring plasmids were subjected to next-generation sequencing using the Illumina Miseq platform. Among the 67 CRE isolates, 42 Klebsiella pneumoniae, 10 Serratia marcescens, 6 Enterobacter cloacae, 2 Raoultella ornithinolytica, 2 K. oxytoca, 1 K. aerogenes, and 4 Escherichia coli isolates were identified. Six different carbapenemases were detected, including bla_KPC-2 (n = 45), bla_KPC-3 (n = 1), bla_NDM-1 (n = 6), bla_NDM-5 (n = 1), bla_IMP-4 (n = 2), and bla_VIM-1 (n = 2); bla_OXA-48-like genes were not detected. One E. cloacae strain possessed both bla_NDM-1 and bla_KPC-3, while two E. cloacae isolates harbored bla_NDM-1 and bla_VIM-1. ESBLs (CTX-M, SHV, and TEM) and/or AmpC (CMY, DHA, and ACT/MIR) genes were also identified in 59 isolates, including 13 strains that lacked carbapenemases. Several insertions or stop codon mutations were found within porin genes of K. pneumoniae, E. coli and S. marcescens isolates, both with and without carbapenemases. The 42 K. pneumoniae isolates belonged to 12 different sequence types (ST), with ST11 being the most common, while the 6 E. cloacae isolates comprised 4 different STs. The 10 S. marcescens all shared the same PFGE pulsotype, suggestive of clonal spread. Complete plasmid sequencing and PCR screening revealed both intra-strain and inter-species spread of a common bla_KPC-2-harboring plasmid in our hospital. Taken together, our study revealed extensive genetic diversity among CRE isolates form a single Chinese hospital. CRE isolates circulating in the hospital differ significantly in their species, STs, porin genes, carbapenemase genes, and their plasmid content, highlighting the complex dissemination of CRE in this endemic region.

Characterize carbapenem-resistant Klebsiella pneumoniae isolates for nosocomial pneumonia and their Gram-negative bacteria neighbors in the respiratory tract

This study was conducted to perform an epidemiological survey of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates for nosocomial pneumonia (NP) and visit their Gram-negative bacteria neighbors (GNNs) from the respiratory tracts. Pulsed-field gel electrophoresis and multi locus sequence typing were performed to evaluate the clonal relationships of these isolates. Statistical methods were then used to understand their possible relationship between CRKP and their GNNs. Among the 63 CRKP isolates, 84.1% produced a KPC-2 carbapenemase gene, followed by blaNDM-1 and blaIMP-38 like. 13 different STs and 29 clones were identified. Less heterogeneous clone backgrounds were observed in 53 KPC-2 K. pneumoniae isolates, and 6 STs have been found to contain KPC-2, of which the predominant ST11 harbored 47 KPC-2-producing K. pneumoniae isolates. Particularly, the two infrequent isolates co-possessing blaKPC-2 and blaIMP-38 like shared a different clonal relationship. 87 GNNs isolates of CRKP were established, the analysis present that different strains showed significant or no difference with CRKP upon antibiotics susceptibility. Conclusion, ST11 harboring KPC-2-producing K. pneumoniae isolates were dominant for NP, and both clonal spread and horizontal transfer contributed to the dissemination of CRKP. However, additional studies are needed to explore the biological relationship with their GNNs.

Early emergence of OXA-181-producing Escherichia coli ST410 in China

OBJECTIVES

The aim of this study was to investigate the prevalence and characterisation of OXA-48-like-producing Enterobacteriaceae in Henan Province, China.

METHODS

A total of 339 carbapenem-non-susceptible clinical Enterobacteriaceae isolates [imipenem or meropenem minimum inhibitory concentration (MIC) of >1μg/mL] obtained between January 2013 and December 2016 were screened for the presence of the bla_OXA-48-like gene by PCR and sequencing. Antimicrobial susceptibility to various antimicrobials agents was examined by MIC testing. Multilocus sequence typing (MLST) was performed for bacterial genotyping. The plasmid pEC21-OXA-181 was transformed into Escherichia coli DH5α by electroporation and was sequenced using an Illumina MiSeq platform, followed by subsequent annotation and genetic analysis.

RESULTS

Among the 339 carbapenem-non-susceptible Enterobacteriaceae isolates, only one (0.3%) E. coli strain EC21, belonging to ST410, was positive for bla_OXA-181, a variant of bla_OXA-48. This OXA-181-producing E. coli, recovered from a patient without a history of foreign travel, was obtained earlier than the first reported bla_OXA-181-positive E. coli (WCHEC14828) in Sichuan Province, China. Plasmid analysis revealed that bla_OXA-181 together with the quinolone resistance gene qnrS1 was carried by an IS26-flanked composite transposon on a 51-kb IncX3-type plasmid.

CONCLUSIONS

These findings indicate the emergence of OXA-181-producing E. coli in China earlier than previously thought. The bla_OXA-181 gene is associated with the widely disseminated potentially endemic E. coli ST410 clone and is carried by an IncX3 plasmid, a common vehicle for spreading NDM-type carbapenemases, which might promote the further dissemination of bla_OXA-181 among the Enterobacteriaceae in China.

Coexistence of NDM-1-producing Escherichia coli and Citrobacter freundii in the same patient

OBJECTIVES

Although bla_NDM-1 has been widely detected in various Enterobacteriaceae clinical isolates, multiple bla_NDM-1 colonisations within the same patient remain rare. The aim of the study was to describe a patient with respiratory tract colonisation with NDM-1-producing Escherichia coli and Citrobacter freundii during hospitalisation in China.

METHODS

Two carbapenem-resistant isolates were analysed. Antimicrobial susceptibility testing, metallo-β-lactamase production, conjugation assay, plasmid analysis and molecular typing were performed.

RESULTS

The two clinical isolates carried the bla_NDM-1 gene and showed resistance to carbapenems. S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) revealed that E. coli NB753 harboured a plasmid of ca. 80kb, and C. freundii NB865 harboured three plasmids (ca. 70, 80 and 135kb). Southern blot and Inc replicon typing further demonstrated that both isolates carried the bla_NDM-1 gene on a self-transferrable IncX3 plasmid. Moreover, the two NDM-producing plasmids were conjugative and the transconjugants showed increased resistance to carbapenems.

CONCLUSION

An NDM-1-encoding plasmid harboured by various clinical isolates in a single patient is worrying considering that this plasmid may be widespread in our hospital. Furthermore, the threat of carbapenemase-producing bacterial epidemics should be closely monitored. However, a limitation of this study was the extremely small sample size.

Multidrug Resistance Mechanisms of Carbapenem Resistant Klebsiella pneumoniae Strains Isolated in Chongqing, China

BACKGROUND

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is considered a serious global threat. However, little is known regarding the multidrug resistance (MDR) mechanisms of CRKP. This study investigated the phenotypes and MDR mechanisms of CRKP and identified their clonal characteristics.

METHODS

PCR and sequencing were utilized to identify antibiotic resistance determinants. Integron gene cassette arrays were determined by restriction fragment length polymorphism (RFLP) analysis. Multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were used for epidemiological analysis. Plasmids were typed by using a PCR-based replicon typing and analyzed by conjugation and transformation assays.

RESULTS

Seventy-eight strains were identified as resistant to at least one carbapenem; these CRKP strains had a high prevalence rate (38.5%, 30/78) of carbapenemase producers. Additionally, most isolates harbored MDR genes, including Extended spectrum β-lactamases (ESBLs), AmpC, and quinolone and aminoglycoside resistance genes. Loss of porin genes was observed, and Class 1 integron was detected in 66.7% of the investigated isolates. PFGE and MLST results excluded the occurrence of clonal dissemination among these isolates.

CONCLUSIONS

A high prevalence of NDM-1 genes encoding carbapenem resistance determinants was demonstrated among the K. pneumoniae isolates. Importantly, this is the first report of bla(NDM-1) carriage in a K. pneumoniae ST1383 clone in China and of a MDR CRKP isolate co-harboring bla(NDM-1), bla(KPC-2), bla(CTX-M), bla(SHV), acc(6')-Ib, rmtB, qnrB, and acc(6')-Ib-cr.

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-β-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, bla_NDM-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.

Review of antibiotic resistance in China and its environment

Antibiotic resistance is a global health crisis linked to increased, and often unrestricted, antibiotic use in humans and animals. As one of the world's largest producers and consumers of antibiotics, China is witness to some of the most acute symptoms of this crisis. Antibiotics and antibiotic resistance genes (ARGs) are widely distributed in surface water, sewage treatment plant effluent, soils and animal wastes. The emergence and increased prevalence of ARGs in the clinic/hospitals, especially carbapenem-resistant gram negative bacteria, has raised the concern of public health officials. It is important to understand the current state of antibiotic use in China and its relationship to ARG prevalence and diversity in the environment. Here we review these relationships and their relevance to antimicrobial resistance (AMR) trends witnessed in the clinical setting. This review highlights the issues of enrichment and dissemination of ARGs in the environment, and also future needs in mitigating the spread of antibiotic resistance in the environment, particularly under the 'planetary health' perspective, i.e., the systems that sustain or threaten human health.

Mechanisms of fosfomycin resistance in carbapenem-resistant Enterobacter sp

We report on fosfomycin susceptibility and mechanisms of resistance in clinical strains of bla_KPC-positive Enterobacter sp. (n = 19). A total of 14 strains (74%) were susceptible to fosfomycin; 8 strains (42%) were positive for fosA and no strains were positive for FosA3 or FosC2. FosA presence does not appear to correlate with susceptibility.

Epidemiology of Carbapenem-Resistant Klebsiella pneumoniae Bloodstream Infections in a Chinese Children's Hospital: Predominance of New Delhi Metallo-β-Lactamase-1

The spread of carbapenem-resistant Klebsiella pneumoniae (CRKp) has become a significant problem worldwide; however, relevant data in children are limited. We performed a retrospective study to better understand the epidemiology of CRKp bloodstream infections at Beijing Children's Hospital. A total of 164 K. pneumoniae strains were collected from blood cultures between January 2011 and September 2014, of which 52 (31.7%) were CRKp strains. All 52 CRKp strains were multidrug resistant; 46 (88.5%) and 49 (94.2%) isolates were resistant to meropenem and imipenem, respectively. Low rates of resistance to amikacin (5.8%), levofloxacin (7.7%), and ciprofloxacin (15.4%) were observed. All isolates were susceptible to colistin. Among the tested carbapenem resistance genes, the predominant gene was bla_NDM-1, detected in 28 (53.8%) isolates, followed by bla_IMP-4 (19, 36.5%) and bla_KPC-2 (4, 7.7%). Multilocus sequence typing identified 31 sequence types (STs), the most predominant of which was ST782 (9, 29.0%). All ST782 strains were New Delhi metallo-β-lactamase-1 (NDM-1) producing. Four novel STs (ST2010, ST2011, ST2012, and ST2013) and two novel alleles (phoE243 and tonB324) were also detected. Hematologic disease was the most common underlying disease (73.1%). All children received initial empirical therapy. A total of 59.6% (31/52) patients received inappropriate empirical therapy, and 45.2% (14/31) changed antimicrobial therapy after blood culture results were obtained. The overall mortality rate was 11.5%. In conclusion, we observed a high rate of CRKp isolates collected from blood cultures and the predominance of NDM-1-producing K. pneumoniae among children from 2011 to 2014.