Coexistence of and Truncated on Different Plasmids in a Isolate in China.
Xie Lianyan,Dou Yi,Zhou Kaixin,Chen Yue,Han Lizhong,Guo Xiaokui,Sun Jingyong
Frontiers in microbiology
To describe the genetic environment, transferability, and antibiotic susceptibility of one clinical isolate harboring both and on different plasmids from a Chinese hospital. The isolate was subjected to antimicrobial susceptibility testing and multilocus sequence typing using Etest and PCR. The plasmids harboring and were analyzed through conjugation experiments, S1-nuclease pulsed-field gel electrophoresis, and hybridization with specific probes. Plasmid DNA was sequenced using Pacbio RS II and annotated using RAST. RJ119, carrying both and , was resistant to almost all carbapenems, cephalosporins, fluoroquinolone, and aminoglycosides and belonged to ST307. was located on a 61,748-bp IncL/M conjugative plasmid, which displayed overall nucleotide identity (99%) to pKPN-E1-Nr.7. was located on a 335,317-bp conjugative plasmid, which was a fusion of a -harboring InA/C plasmid pNDM-US (140,825 bp, 99% identity) and an IncFIB plasmid pKPN-c22 (178,563 bp, 99% identity). The transconjugant RJ119-1 harboring was susceptible to carbapenem, and there was an insertion of IS into the gene. This is the first report of the coexistence of and in one clinical isolate in China. OXA-48 in RJ119 contributed to the majority to its high resistance to carbapenems, whereas NDM-1 remained unexpressed, most likely due to the insertion of IS. Our results provide new insight for the relationship between genetic diagnosis and clinical treatment. They also indicate that increased surveillance of is urgently needed in China.
10.3389/fmicb.2017.00133
Molecular epidemiology of NDM-1- and OXA-48-producing Klebsiella pneumoniae in an Iranian hospital: clonal dissemination of ST11 and ST893.
Solgi Hamid,Badmasti Farzad,Giske Christian G,Aghamohammad Shadi,Shahcheraghi Fereshteh
The Journal of antimicrobial chemotherapy
Objectives:Despite the fact that the blaOXA-48 and blaNDM-1 genes have successfully disseminated among Klebsiella pneumoniae isolates worldwide, outbreaks remain unidentified in Iran. Here we examined the molecular epidemiology of 96 carbapenem-resistant K. pneumoniae recovered from an Iranian hospital. Methods:A total of 96 non-replicate carbapenem-resistant K. pneumoniae were recovered from clinical specimens in a university hospital. Detection of ESBLs and carbapenemases produced by studied strains was performed using PCR and DNA sequencing. The bacterial isolates were assigned to clonal lineages by PFGE and MLST. In addition, plasmids were analysed by PCR-based replicon typing and conjugation assays. Results:All isolates harboured blaOXA-48 and blaNDM-1 genes together or alone. Almost all strains also carried ESBL genes. Eighty-seven isolates of K. pneumoniae were categorized into seven pulsotypes. The predominant strain clusters/pulsotypes associated with the outbreak corresponded to ST11 (48/96) and ST893 (31/96). Plasmids carrying blaOXA-48 and blaNDM-1 were successfully transferred to Escherichia coli K12 as the recipient strain. blaOXA-48 was located on IncL/M plasmids of ∼39 kb, while blaNDM-1 was carried by either an IncFII plasmid of ∼50 kb or an untypeable plasmid of ∼4 or 10 kb. Conclusions:We describe two separate outbreaks of blaOXA-48- and blaNDM-1-carrying K. pneumoniae strains associated with dissemination of the ST11 and ST893 clones, with the ICU acting as the epicentre. The spread of plasmids carrying carbapenemase genes resulting in fulminant antimicrobial resistance is a severe concern.
10.1093/jac/dky081
Hypervirulent Klebsiella pneumoniae: An update on epidemiology, detection and antibiotic resistance.
Acta microbiologica et immunologica Hungarica
Klebsiella pneumoniae is a major human pathogen as it is responsible for various infections. In the past years hypervirulent K. pneumoniae (hvKP) emerged and disseminated worldwide. In this review a summary will be given about epidemiology, detection and antibiotic resistance of hypervirulent K. pneumoniae. A common feature of hypervirulent K. pneumoniae is a combined expression of several virulence factors. A mucoviscosus phenotype, certain capsulare serotypes (e.g.: K1, K2, K28, K47, K63) together with additional genetic markers namely, magA, rmpA or iucABCD, are needed in combinations to achieve the hypervirulent pathotype. Plasmid coded virulence determinants are also detected, that indicates horizontal gene transfer of hypervirulence factors in K. pneumoniae.Interestingly, infections caused by hypervirulent K. pneumoniae occur usually in the community in otherwise healthy people, and during these infections multiple infection sites are detected. Clinical pictures include both invasive infections and local abscess formation. Pyogenic liver abscess is the most frequently reported clinical manifestation and abscess formation in brain, spleen and lung are also diagnosed. Additionally, meningitis, endophthalmitis, trombophlebitis, pneumonia can also develop.In the early reports, hypervirulent K. pneumoniae strains exhibited enhanced virulence but these were susceptible to commonly used antibiotics. However, recently KPC, VIM, NDM and OXA-48 carbapenemase producing hypervirulent K. pneumoniae strains are increasingly reported, furthermore, well-known high-risk K. pneumoniae clones (e.g.: ST11, ST147, ST307) can develop hypervirulent pathotype, that poses an even more alarming challenge.
10.1556/030.2023.02186
Investigation of carbapenem-resistant Klebsiella pneumoniae in Taiwan revealed strains co-harbouring bla and bla and a novel plasmid co-carrying bla and bla.
International journal of antimicrobial agents
The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) is related to the transmission of carbapenemase genes. Strains carrying more than one carbapenemase with a broadened spectrum of antibiotic resistance have been detected, which is concerning. Although bla-encoding ST11-KL47/KL64 strains are dominant, other clones are emerging. This study investigated 137 CRKP from patients' blood samples in Taiwan. Polymerase chain reaction (PCR) was used to identify carbapenemase genes and capsular (KL) types. Most strains (56%, 77/137) possessed bla alone; however, 12% (17/137) carried bla+bla and these strains showed high resistance to imipenem and meropenem. Strains carrying bla+bla predominantly belonged to KL51 (n=15), followed by KL64 (n=1) and KL47 (n=1). Whole-genome sequencing of one KL51 strain indicated that bla and bla are carried on two different plasmids. PCR was performed using specific primers located in these plasmids, and all bla+bla-encoding strains except the KL64 strain were considered to carry the two abovementioned plasmids. Genome analysis for the KL64 strain revealed that bla and bla are encoded in one plasmid. Notably, the KL51 bla plasmid shared high sequence similarity with the KL64 bla+bla plasmid, except the KL64 plasmid comprised a 15,040-bp insertion encoding bla. The data revealed KL51 as a predominant KL type carrying bla+bla, and identified a novel plasmid carrying bla+bla, highlighting the spread of specific plasmids and clones of CRKP in Taiwan.
10.1016/j.ijantimicag.2023.106964
Activity of polymyxin B combinations against genetically well-characterised Klebsiella pneumoniae producing NDM-1 and OXA-48-like carbapenemases.
International journal of antimicrobial agents
BACKGROUND:Combination therapy can enhance the activity of available antibiotics against multidrug-resistant Gram-negative bacteria. This study assessed the effects of polymyxin B combinations against carbapenemase-producing Klebsiella pneumoniae (K. pneumoniae). METHODS:Twenty clinical K. pneumoniae strains producing NDM-1 (n = 8), OXA-48-like (n = 10), or both NDM-1 and OXA-48-like (n = 2) carbapenemases were used. Whole-genome sequencing was applied to detect resistance genes (e.g. encoding antibiotic-degrading enzymes) and sequence alterations influencing permeability or efflux. The activity of polymyxin B in combination with aztreonam, fosfomycin, meropenem, minocycline, or rifampicin was investigated in 24-hour time-lapse microscopy experiments. Endpoint samples were spotted on plates with and without polymyxin B at 4 x MIC to assess resistance development. Finally, associations between synergy and bacterial genetic traits were explored. RESULTS:Synergistic and bactericidal effects were observed with polymyxin B in combination with all other antibiotics: aztreonam (11 of 20 strains), fosfomycin (16 of 20), meropenem (10 of 20), minocycline (18 of 20), and rifampicin (15 of 20). Synergy was found with polymyxin B in combination with fosfomycin, minocycline, or rifampicin against all nine polymyxin-resistant strains. Wildtype mgrB was associated with polymyxin B and aztreonam synergy (P = 0.0499). An absence of arr-2 and arr-3 was associated with synergy of polymyxin B and rifampicin (P = 0.0260). Emergence of populations with reduced polymyxin B susceptibility was most frequently observed with aztreonam and meropenem. CONCLUSION:Combinations of polymyxin B and minocycline or rifampicin were most active against the tested NDM-1 and OXA-48-like-producing K. pneumoniae. Biologically plausible genotype-phenotype associations were found. Such information might accelerate the search for promising combinations and guide individualised treatment.
10.1016/j.ijantimicag.2023.106967
Emergence of OXA-48-Producing Klebsiella pneumoniae in Taiwan.
Ma Ling,Wang Jann-Tay,Wu Tsu-Lan,Siu L Kristopher,Chuang Yin-Ching,Lin Jung-Chung,Lu Min-Chi,Lu Po-Liang
PloS one
The isolation of OXA-48-producing Enterobacteriaceae has increased dramatically in Mediterranean countries in the past 10 years, and has recently emerged in Asia. Between January 2012 and May 2014, a total of 760 carbapenem non-susceptible Klebsiella pneumoniae (CnSKP) isolates were collected during a Taiwan national surveillance. Carbapenemases were detected in 210 CnSKP isolates (27.6%), including 162 KPC-2 (n = 1), KPC-3, KPC-17, and NDM-1 (n = 1 each), OXA-48 (n = 4), IMP-8 (n = 18), and VIM-1 (n = 24). The four blaOXA-48 CnSKP isolates were detected in late 2013. Herein we report the emergence OXA-48-producing K. pneumoniae isolates in Taiwan. PFGE analysis revealed that the four isolates belonged to three different pulsotypes. Three isolates harboured blaCTX-M genes and belonged to MLST type ST11. In addition, the plasmids belonged to the incompatibility group, IncA/C. One isolate belonged to ST116 and the plasmid incompatibility group was non-typeable. The sequence upstream of the blaOXA-48 gene in all four isolates was identical to pKPOXA-48N1, a blaOXA-48-carrying plasmid. This is the first report of OXA-48-producing Enterobacteriaceae in Taiwan and the second report to identify blaOXA-48 on an IncA/C plasmid in K. pneumoniae. Given that three isolates belong to the same pandemic clone (ST11) and possess the IncA/C plasmid and similar plasmid digestion profile that indicated the role of clonal spread or plasmid for dissemination of blaOXA-48 gene, the emergence of OXA-48-producing K. pneumoniae in Taiwan is of great concern.
10.1371/journal.pone.0139152
High prevalence of OXA-48-like and NDM carbapenemases among carbapenem resistant of clinical origin from Iran.
Iranian journal of microbiology
Background and Objectives: is increasingly developing resistance to last-resort antibiotics such as carbapenems. This study aimed to investigate the dissemination of common carbapenemase encoding genes among 48 clinical isolates of carbapenem-resistant (CRKP). Materials and Methods:Antimicrobial susceptibility testing was performed by broth dilution and disc diffusion methods. The phenotypic evaluation of carbapenemase production was performed by using Modified Carbapenem Inactivation Method. Presence of carbapenemase encoding genes , , , , and was screened by PCR. Results:Overall, carbapenemases were produced in all CRKP isolates. The and were the most prevalent genes detected among all and 66.6% (n=32) of CRKP isolates respectively. The was detected in only one isolate co-harboring NDM and OXA-48-like carbapenemases. The and genes were not identified in any of the isolates. While tigecycline was the most active agent against CRKP isolates with low resistance rate (4.1%), high rate of resistance was observed to colistin (66.6%), amikacin (79%) and most of other tested antimicrobials. Conclusion:Our results revealed predominant prevalence of OXA-48-like and NDM carbapenemases among CRKP clinical isolates. High rate of resistance to last-resort agents such as colistin among CRKP isolates is a source of great concern.
10.18502/ijm.v15i5.13866
Detection of NDM-1/5 and OXA-48 co-producing extensively drug-resistant hypervirulent Klebsiella pneumoniae in Northern Italy.
Journal of global antimicrobial resistance
OBJECTIVES:Using a hybrid long-read sequencing approach, we aimed to fully characterise four extensively-drug resistant (XDR) hypervirulent Klebsiella pneumoniae isolates, one of which represented the first strain isolated in Italy co-expressing NDM-1/5 and OXA-48 carbapenemases. METHODS:Whole-genome sequencing was performed using Illumina and Oxford Nanopore Technology platforms. An assembly pipeline was used to recover the structures both of the chromosome and plasmids. RESULTS:Multilocus sequence typing (MLST) showed that these strains belonged to high-risk sequence types (STs) not commonly circulating in Italy (ST383, ST147 and ST15). The hybrid sequencing approach allowed to characterise three multidrug resistance plasmids, which demonstrated high homology with previously sequenced plasmids, that were simultaneously detected in one ST383 strain carrying, respectively, bla, bla and bla. CONCLUSION:This is the first report in Italy of new hypervirulent XDR K. pneumoniae clones characterised by co-production of OXA-48, NDM-1 and NDM-5. The discovery of new high-risk clones harbouring multiple mobile elements is a growing problem that poses a great challenge for public health.
10.1016/j.jgar.2022.01.001
Investigation of NDM-1 and OXA-48 producing carbapenem resistant Klebsiella pneumoniae ST15 in Iran.
Acta microbiologica et immunologica Hungarica
The aim of this study was to determine the frequency of carbapenem resistant Klebsiella pneumoniae (CRKP) sequence types (STs) in Iran. Samples were collected from three university hospitals in Sanandaj, Iran, from December 2016 to March 2018. Antibiotic susceptibility testing, phenotypic and genotypic detection of carbapenemases were performed. Common K. pneumoniae capsular types were sought for all isolates. The genetic relatedness of isolates was investigated by multilocus sequence typing (MLST). Plasmids were detected by PCR-based Replicon Typing (PBRT). During the study, 67 K. pneumoniae isolates were identified. Of which, 18 (26.9%) isolates were detected as carbapenem-resistant. The most effective antibacterial agent was tigecycline (97%, 65 isolates) followed by imipenem and ertapenem (73.13%, 49 isolates). PCR showed that 13 isolates (19.4%) had blaNDM-1 gene and 5 (7.5%) harbored blaOXA-48. Examination of common capsular types showed that 2 isolates had K2 and 2 others had K54. REP-PCR revealed 10 clones and 11 singleton strains. MLST analysis of CRKP found ST15 as the most common type (13 isolates, 72.2%), but other STs were also detected namely, ST19, ST117, ST1390, and ST1594. ColE1 and IncL/M plasmids were the carriers of blaNDM-1 and blaOXA-48, respectively. The results showed that CRKP spread in our health centers. Our results, therefore, indicate a worrying trend of resistance to carbapenems in K. pneumoniae.
10.1556/030.2023.01945
High frequency of NDM-1 and OXA-48 carbapenemase genes among Klebsiella pneumoniae isolates in central Iran.
BMC microbiology
BACKGROUND:The emergence and distribution of multidrug-resistant (MDR) and carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a global health threat. Therefore, this study aimed to investigate the frequency and antibiotic resistance patterns of MDR, extensively drug-resistant (XDR), and CRKP, as well as the antibiotic resistance genes of Klebsiella pneumoniae (K. pneumoniae) isolates from patients' infectious samples from central Iran. METHODS:This study examined 546 clinical samples of patients to identify K. pneumoniae. The isolates were investigated for their antibiotic resistance profile, extended-spectrum β-lactamase (ESBL), AMPC β-lactamase, carbapenemase resistance, sulfonamide, tetracycline, plasmid-mediated quinolone resistance (PMQR) along with their resistance genes, integrase, and quaternary ammonium compounds (qac) by polymerase chain reaction (PCR). RESULTS:Out of 546 clinical samples, 121 (22.1%) cases of K. pneumoniae were identified using culture and PCR methods. The highest antibiotic resistance rates were found for ampicillin (119/121; 98.3%), cotrimoxazole (78/121; 64.4%), and cefixime, cefotaxime, ceftriaxone, and ceftazidime as a group (77/121; 63.6%). Tigecycline, colistin, and fosfomycin were the most effective antimicrobial agents with 98.4%, 96.7%, and 95.9% susceptibility, respectively. The amount of CRKP was 51 (42.1%). All CRKP isolates were MDR. The most abundant genes were bla (77/77; 100%), bla (76/77; 98.7%), bla (76/77; 98.7%), bla (73/77; 94.8%) for ESBL; bla 28 (48.3%) and bla 26 (44.8%) for AMPC β-lactamase; and bla 46 (90.1%) and bla 36 (70.5%) for carbapenemase. Among the PMQR determinants, qnrB (25/52; 48%), qnrS (19/52; 36.5%), and qnrA (11/52; 21.1%) were positive from the isolates. TetA and tetB were recognized in 25 (44.6%) and 17 (30.3%) isolates, respectively. Class 1 and 2 integrons were recognized in 97 (80.1%) and 53 (43.8%) isolates, respectively. CONCLUSIONS:Due to the high prevalence of MDR and CRKP in central Iran, tracking and immediate intervention are necessary for control and inhibition of K. pneumoniae resistant isolates. Tigecycline, colistin, and fosfomycin are the best treatment options for treatment of patients with CRKP in this geographical area.
10.1186/s12866-023-02840-x
Emergence of Klebsiella pneumoniae ST11 co-producing NDM-1 and OXA-48 carbapenemases in Greece.
Protonotariou Efthymia,Meletis Georgios,Chatzopoulou Fani,Malousi Andigoni,Chatzidimitriou Dimitrios,Skoura Lemonia
Journal of global antimicrobial resistance
OBJECTIVES:Klebsiella pneumoniae is a well-known pathogen frequently implicated in serious life-threatening nosocomial infections. Here we present a K. pneumoniae isolate (AHEPA1046) co-harbouring bla and bla isolated from a blood sample of an inpatient in Thessaloniki, Greece. METHODS:Whole-genome sequencing (WGS) was performed using an Illumina MiniSeq Sequencing System. Multilocus sequence typing (MLST) was performed using a BLAST-based approach, and antimicrobial resistance genes and plasmid replicons were identified by ResFinder and PlasmidFinder, respectively. The Rapid Annotation using Subsystem Technology (RAST) v.2.0 server was used for genome annotation. RESULTS:WGS analysis revealed the complete resistome of K. pneumoniae AHEPA1046. The strain harboured bla and bla together with 16 additional antimicrobial resistance genes and was resistant to carbapenems, aminoglycosides, quinolones, macrolides, tetracyclines, trimethoprim, fosfomycin and phenicols. Moreover, it was classified as ST11. CONCLUSION:This is the first report of a K. pneumoniae clinical isolate from Greece co-producing NDM-1 and OXA-48 carbapenemases and is one of a few reported worldwide.
10.1016/j.jgar.2019.08.020
Carbapenem-resistant hypermucoviscous clinical isolates from a tertiary hospital in China: Antimicrobial susceptibility, resistance phenotype, epidemiological characteristics, microbial virulence, and risk factors.
Frontiers in cellular and infection microbiology
Hypervirulent and multidrug-resistant poses a significant threat to public health. We aimed to determine the common carbapenemase genotypes and the carriage patterns, main antibiotic resistance mechanisms, and susceptibility of clinical isolates of carbapenem-resistant (CRKP) to ceftazidime/avibactam (CZA) for the reasonable selection of antimicrobial agents and determine whether hypermucoviscous (HMV) phenotype and virulence-associated genes are key factors for CRKP colonization and persistence. Antibiotics susceptibility of clinical CRKP isolates and carbapenemase types were detected. CRKP isolates were identified as hypermucoviscous (HMKP) using the string test, and detection of virulence gene was performed using capsular serotyping. The , , , and/or were detected in 96.4% (402/417) of the isolates, and the (64.7%, 260/402) was significantly higher (<0.05) than those of (25.1%), (10.4%), and (4.2%). Carriage of a single carbapenemase gene was observed in 96.3% of the isolates, making it the dominant antibiotic resistance genotype carriage pattern ( < 0.05). Approximately 3.7% of the isolates carried two or more carbapenemase genotypes, with + and + being the dominant multiple antibiotic resistance genotype. In addition, 43 CRKP isolates were identified as HMKP, with a prevalence of 10.3% and 2.7% among CRKP and all isolates, respectively. Most clinical CRKP isolates were isolated from elderly patients, and carbapenemase production was the main mechanism of drug resistance. Tigecycline and polymyxin B exhibited exceptional antimicrobial activity against CRKP isolates . Furthermore, , , and were the main carbapenemase genes carried by the CRKP isolates. CZA demonstrated excellent antimicrobial activity against isolates carrying the single or genotype. Capsular serotype K2 was the main capsular serotype of the carbapenem-resistant HMKP isolates. Survival rates of injected with 1-7 were 20.0, 16.7, 6.7, 23.3, 16.7, 3.3, and 13.3, respectively. Therefore, worldwide surveillance of these novel CRKP isolates and carbapenem-resistant HMKP isolates as well as the implementation of stricter control measures are needed to prevent further dissemination in hospital settings.
10.3389/fcimb.2022.1083009
Molecular and Clinical Characteristics of Carbapenem-Resistant Isolates at a Tertiary Hospital in Wuhan, China.
Infection and drug resistance
Background:Carbapenem resistant Klebsiella pneumoniae (CRKP) is an independent risk factor for nosocomial infection which poses a serious threat to human health. How to prevent and suppress CRKP infection and explore its drug resistance mechanisms have become a huge challenge and possesses immediate significance. Methods:A total of 45 CRKP strains isolated from hospitalized patients in Zhongnan Hospital of Wuhan University were collected from August 2018-December 2020. The strain's identification and antimicrobial susceptibility tests were performed using the VITEK 2 automated identification instrument. Single molecule DNA sequencing of 45 CRKP isolates was performed by the third generation high-throughput sequencing technology. Results:The results were analyzed by multi locus sequence typing (MLST) and phylogenetic analysis. Antimicrobial susceptibility showed that 45 CRKP isolates were multi-drug resistant strains, and the resistance rates to common antibiotics were as high as 68%. Whole genome sequencing results showed that the CRKP strains carried multiple drug resistance genes and virulence factors. MLST analysis found two different sequence types (ST), of which 44 were ST11 and 1 was ST1049. Conclusion:Through whole genome sequencing (WGS), we found multiple drug-resistant genes and virulence factors, and there was obvious dominant microbiota. The source was mainly related to nosocomial infection. The ST11-KPC Klebsiella pneumoniae was the main type, which was consistent with the most common type in China. We identified several dominant microbiotas which may serve as a target in the clinical prevention and treatment of severe bacterial infections. Our finding may have a role for guiding clinical antibiotic choosing.
10.2147/IDR.S397975