High frequency of multidrug-resistant (MDR) Klebsiella pneumoniae harboring several β-lactamase and integron genes collected from several hospitals in the north of Iran

Analysis of mcr family of colistin resistance genes in Gram-negative isolates from a tertiary care hospital in India

AIM

Colistin serves as the drug of last resort for combating numerous multidrug-resistant (MDR) Gram-negative infections. Its efficacy is hampered by the prevalent issue of colistin resistance, which severely limits treatment options for critically ill patients. Identifying resistance genes is crucial for controlling resistance spread, with horizontal gene transfer being the primary mechanism among bacteria. This study aimed to assess the prevalence of plasmid-mediated mcr genes associated with colistin resistance in Gram-negative bacteria, utilizing both genotypic and phenotypic tests.

METHODS AND RESULTS

The clinical isolates (n = 913) were obtained from a tertiary care center in Chennai, India. Colistin resistance was seen among Gram-negative isolates. These strains underwent screening for mcr-1, mcr-3, mcr-4, and mcr-5 genes via conventional PCR. Additionally, mcr-positive isolates were confirmed through Sanger sequencing and phenotypic testing. The bacterial isolates predominantly comprised Klebsiella pneumoniae (62.43%), Escherichia coli (19.71%), Pseudomonas aeruginosa (10.73%), and Acinetobacter baumannii (4.81%), along with other species. All isolates exhibited multidrug resistance to three or more antibiotic classes. Colistin resistance, determined via broth microdilution (BMD) using CLSI guidelines, was observed in 13.08% of the isolates studied. Notably, mcr-5 was detected in K. pneumoniae in PCR, despite its absence in Sanger sequencing and phenotypic tests (including the combined-disk test, colistin MIC in the presence of EDTA, and Zeta potential assays). This finding underscores the importance of employing multiple diagnostic approaches to accurately identify colistin resistance mechanisms.

Effect of biogenic bismuth nanoparticle on the expression of New Delhi metallo-β-lactamase (NDM) gene in Multidrug-Resistant Klebsiella pneumoniae

Aim and background

The emergence of Multidrug-Resistant Klebsiella pneumoniae is a global concern due to high mortality and treatment challenges. One of the most important genes for resistance is NDM, which makes the organism resistant to most antibiotics. Today, the use of nanoparticles as therapeutic options has stimulated researchers around the world to investigate its effects. The aim of this study was to investigate the effects of biosynthesized bismuth nanoparticles (Bi NPs) on the expression of NDM genes in multidrug-resistant K. pneumoniae.

Materials and methods

In this study, 5 multidrug-resistant K. pneumoniae clinical isolates from patients referred to Afzalipour Hospital in Kerman, Iran, were used. Antibiotic sensitivity test was performed by disc diffusion method. The presence of the NDM gene was checked in isolates using a PCR reaction. The isolates containing the NDM gene were exposed to the biosynthesized and characterized bismuth nanoparticles, and the effects on the expression of the NDM gene was investigated using real-time PCR.

Results

The results showed that 3 isolates of K. pneumoniae had NDM genes. In TEM and SEM analysis showed that the nanoparticles had a spherical structure and an average size of 22.36 nm. The investigation of biogenic Bi NPs on the expression of the NDM gene demonstrated that the samples treated with bismuth nanoparticles decreased the expression of the NDM gene by 1.6 times compared to the control group (p < 0.011).

Conclusion

Our findings showed that biosynthesized Bi NPs have a high potential to deal with antibiotic resistance genes and can be a promising for treatment.

Antibiotic Resistance, Biofilm Formation, and Persistent Phenotype of Klebsiella pneumoniae in a Vietnamese Tertiary Hospital: A Focus on Amikacin

Klebsiella pneumoniae stands out as a major opportunistic pathogen responsible for both hospital- and community-acquired bacterial infections. This study comprehensively assesses the antibiotic resistance, amikacin persistent patterns, and biofilm-forming ability of 247 isolates of K. pneumoniae obtained from an intensive care unit of a tertiary hospital in Vietnam. Microdilution assays, conducted on a 96-well plate, determined the minimum inhibitory concentrations (MICs) of amikacin. Susceptibility data for other antibiotics were gathered from the antibiogram profile. Stationary-phase bacteria were exposed to 50 × MIC, and viable bacteria counts were measured to determine amikacin persistence. Biofilm forming capacity on 96-well polystyrene surfaces was assessed by biomass and viable bacteria. The prevalence of resistance was notably high across most antibiotics, with 64.8% classified as carbapenem-resistant K. pneumoniae and 81.4% as multidrug resistant. Amikacin, however, exhibited a relatively low rate of resistance. Of the isolates, 58.2% demonstrated a moderate to strong biofilm formation capacity, and these were found to be poorly responsive to amikacin. K. pneumoniae reveals a significant inclination for amikacin persistence, with ∼45% of isolates displaying an antibiotic antibiotic-survival ratio exceeding 10%. The study sheds light on challenges in treating of K. pneumoniae infection in Vietnam, encompassing a high prevalence of antibiotic resistance, a substantial ability to form biofilm, and a notable rate of antibiotic persistence.

Emergence of carbapenem resistant gram-negative pathogens with high rate of colistin resistance in Egypt: A cross sectional study to assess resistance trends during the COVID-19 pandemic

The current study investigated the temporal phenotypic and genotypic antimicrobial resistance (AMR) trends among multi-drug resistant and carbapenem-resistant Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa recovered from Egyptian clinical settings between 2020 and 2021. Bacterial identification and antimicrobial sensitivity of 111 clinical isolates against a panel of antibiotics were performed. Molecular screening for antibiotic resistance determinants along with integrons and associated gene cassettes was implemented. An alarming rate (98.2%) of these isolates were found to be phenotypically resistant to carbapenem. Although 23.9 % K. pneumoniae isolates were phenotypically resistant to colistin, no mobile colistin resistance (mcr) genes were detected. Among carbapenem-resistant isolates, blaNDM and blaOXA-48-like were the most prevalent genetic determinants and were significantly overrepresented among K. pneumoniae. Furthermore, 84.78% of K. pneumoniae isolates co-produced these two carbapenemase genes. The plasmid-mediated quinolone resistance genes (qnrS and qnrB) were detected among the bacterial species and were significantly more prevalent among K. pneumoniae. Moreover, Class 1 integron was detected in 82% of the bacterial isolates. This study alarmingly reveals elevated resistance to last-resort antibiotics such as carbapenems as well as colistin which impose a considerable burden in the health care settings in Egypt. Our future work will implement high throughput sequencing-based antimicrobial resistance surveillance analysis for characterization of novel AMR determinants. This information could be applied as a step forward to establish a robust antibiotic stewardship program in Egyptian clinical settings, thereby addressing the rising challenges of AMR.

Whole proteome analysis of MDR Klebsiella pneumoniae to identify mRNA and multiple epitope based vaccine targets against emerging nosocomial and lungs associated infections

Klebsiella pneumonia is a Gram negative facultative anaerobic bacterium involved in various community-acquired pneumonia, nosocomial and lungs associated infections. Frequent usage of several antibiotics and acquired resistance mechanisms has made this bacterium multi-drug resistance (MDR), complicating the treatment of patients. To avoid the spread of this bacterium, there is an urgent need to develop a vaccine based on immuno-informatics approaches that is more efficient than conventional method of vaccine prediction or development. Initially, the complete proteomic sequence of K. pneumonia was picked over for specific and prospective vaccine targets. From the annotation of the whole proteome, eight immunogenic proteins were selected, and these shortlisted proteins were interpreted for CTL, B-cells, and HTL epitopes prediction, to construct mRNA and multi-epitope vaccines. The Antigenicity, allergenicity and toxicity analysis validate the vaccine's design, and its molecular docking was done with immuno-receptor the TLR-3. The docking interaction showed a stronger binding affinity with a minimum energy of -1153.2 kcal/mol and established 23 hydrogen bonds, 3 salt bridges, 1 disulfide bond, and 340 non-binding contacts. Further validation was done using In-silico cloning which shows the highest CAI score of 0.98 with higher GC contents of 72.25% which represents a vaccine construct with a high value of expression in E. coli. Immune Simulation shows that the antibodies (IgM, IgG1, and IgG2) production exceeded 650,000 in 2 to 3 days but the response was completely neutralized in the 5th day. In conclusion, the study provides the effective, safe and stable vaccine construct against Klebsiella pneumonia, which further needs in vitro and in vivo validations.Communicated by Ramaswamy H. Sarma.

Molecular Screening of Carbapenem-Resistant K. pneumoniae (CRKP) Clinical Isolates for Concomitant Occurrence of Beta-Lactam Genes (CTX-M, TEM, and SHV) in the Kingdom of Bahrain

The emergence of extended-spectrum β-lactamase-producing Klebsiella pneumoniae, including CRKP infections, has resulted in significant morbidity and mortality worldwide. We aimed to explore the presence of bla genes (CTX-M, TEM, and SHV) in CRKP isolates. A total of 24 CRKP isolates were randomly selected from the Salmaniya Medical Complex Microbiology Laboratory. These isolates, which were positive for carbapenemases, were further explored for CTX-M, TEM, and SHV genes using PCR. All the CTX-M PCR amplicons were sent for sequencing. To determine genetic relatedness, molecular typing by ERIC-PCR was performed. The bla gene testing demonstrated that a significant proportion of these isolates harbored SHV, CTX-M, and TEM genes (100%, 91.6%, and 45.8%), respectively. Bioinformatic analyses confirmed CTX-M-15 in these isolates. ERIC-PCR analysis showed three clusters demonstrating genetic relatedness. The study findings reveal the concomitant carriage of the SHV and CTX-M-15 and a comparatively lower carriage of TEM genes in CRKP isolates. Our findings highlight the significance of routinely reporting the presence of antibiotic resistance genes along with regular antibiotic sensitivity reports, as this will aid clinicians in prescribing appropriate antibiotics.

Occurrence of some common carbapenemase genes in carbapenem-resistant Klebsiella pneumoniae isolates collected from clinical samples in Tabriz, northwestern Iran

OBJECTIVES

This study aimed to evaluate the antibiotic resistance patterns and prevalence of carbapenemase genes in Klebsiella pneumoniae isolates in different clinical samples from Tabriz city, northwestern Iran.

RESULTS

This cross-sectional study was conducted in the Department of Microbiology, Islamic Azad University, Ahar Branch, Iran, in 2020. K. pneumoniae isolates were collected from different clinical samples, including blood, wounds, sputum, and urine. The isolates were identified using a series of standard bacteriological tests. Antibiotic resistance was determined by the disc diffusion method. The presence of blaVIM, blaNDM, blaKPC, blaOXA, and blaIMP genes were screened by polymerase chain reaction (PCR). A total of 100 non-duplicated K. pneumoniae isolates were collected from 57 urine samples, 27 blood samples, 13 wound samples, and 3 sputum samples. Overall, 70.0% of the samples were from inpatients, while 30.0% were from outpatients. The most resistance rate was related to ampicillin (94.0%), while the lowest resistance rate was related to imipenem (18.0%) and meropenem (20.0%). Overall, 25.0% of the isolates were carbapenem-resistant, of which 13.0% were resistant to both imipenem and meropenem. The PCR showed the total prevalence of 23.0% for carbapenemase genes, including 18.0% for blaKPC, 3.0% for blaVIM, 1.0% for blaIMP, and 1.0% for blaOXA gene. The blaNDM gene was not detected in any isolate. The prevalence of carbapenemase-producing K. pneumoniae isolates was relatively lower in northwestern Iran than in other regions of the country. However, special attention should be paid to the proper use of antibiotics, particularly carbapenems, to prevent further spread of antibiotic resistance and its related genes.

Factors Associated with Extended-Spectrum β-Lactamases and Carbapenem-Resistant Klebsiella pneumoniae Bloodstream Infections: A Five-Year Retrospective Study

Klebsiella pneumoniae is one of the leading causes of nosocomial infections. It has been estimated that nosocomial infection by Klebsiella pneumoniae comprises 3-8% of all nosocomial infections. Klebsiella pneumoniae bloodstream infections (BSIs) occur worldwide with varying mortality. Resistant strains, like those producing extended-spectrum beta-lactamases (ESBL) and carbapenemases, are becoming increasingly common, especially in hospital settings, posing therapeutic challenges. In this article, we aimed to study the epidemiology and risk factors of BSIs due to resistant Klebsiella pneumoniae strains in the period 1 January 2014-31 December 2018 at the Nicosia General Hospital, the largest tertiary hospital in Cyprus. Data on demographics, co-morbidities, prior hospitalization, prior intensive care unit (ICU) admission, previous antimicrobial use, nosocomial acquisition of the infection, the presence of a prosthetic device or surgery, and the primary site of infection were retrospectively recorded. Associations between the detection of ESBL Klebsiella pneumoniae BSIs and factors/covariates were examined using logistic regression. This study involved 175 patients with BSI caused by Klebsiella pneumoniae. Of these, 61 BSIs were caused by ESBL strains, 101 by non-ESBL, and 13 by carbapenem-resistant (CR) strains. In univariable analyses, age, sex, heart disease, antimicrobial use during current admission, previous hospitalization (ward or ICU), and primary BSI were associated with the presence of an ESBL strain. Antibiotic use during current admission and heart disease remained statistically significantly associated with ESBL Klebsiella pneumoniae BSI in multivariable models. Antibiotic use during current admission, respiratory infection, and a recent history of surgery were more prevalent among CR Klebsiella pneumoniae BSI patients than among non-CR Klebsiella pneumoniae BSI patients. Our study showed that recent antimicrobial use and heart disease were associated with BSI due to ESBL-producing Klebsiella pneumoniae. This finding could inform clinical practice in hospital settings.

A Bacteriophage-Loaded Microparticle Laden Topical Gel for the Treatment of Multidrug-Resistant Biofilm-Mediated Burn Wound Infection

Klebsiella pneumoniae is regarded as one of the most profound bacteria isolated from the debilitating injuries caused by burn wounds. In addition, the multidrug resistance (MDR) and biofilm formation make treating burn patients with clinically available antibiotics difficult. Bacteriophage therapy has been proven an effective alternative against biofilm-mediated wound infections caused by MDR bacterial strains. In the current study, the bacteriophage (BPKPФ1) against MDR Klebsiella pneumoniae was isolated and loaded into the chitosan microparticles (CHMPs), which was later incorporated into the Sepineo P 600 to convert into a gel (BPKPФ1-CHMP-gel). BPKPФ1 was characterized for lytic profile, morphological class, and burst size, which revealed that the BPKPФ1 belongs to the family Siphoviridae. Moreover, BPKPФ1 exhibited a narrow host range with 128 PFU/host cell of burst size. The BPKPФ1-loaded CHMPs showed an average particle size of  1.96 ± 0.51 μm, zeta potential 32.16 ± 0.41 mV, and entrapment efficiency in the range of 82.44 ± 1.31%. Further, the in vitro antibacterial and antibiofilm effectiveness of BPKPФ1-CHMPs-gel were examined. The in vivo potential of the BPKPФ1-CHMPs-gel was assessed using a rat model with MDR Klebsiella pneumoniae infected burn wound, which exhibited improved wound contraction (89.22 ± 0.48%) in 28 days with reduced inflammation, in comparison with different controls. Data in hand suggest the potential of bacteriophage therapy to be developed as personalized therapy in case of difficult-to-treat bacterial infections.

Prevalence of extended-spectrum β-lactamase and carbapenem-resistant Klebsiella pneumoniae in clinical samples

OBJECTIVES

To assess the prevalence of these resistant strains in the overall isolates of Klebsiella pneumoniae (K. pneumoniae) in hospital settings.

METHODS

This retrospective study was conducted from November 2020 to November 2021. The identification and antibiotic susceptibility testing were performed using standard laboratory methods according to the EUCAST standards. The detection of ESBL and carbapenemase production was performed using phenotypic methods such as E-test, combined-disk test with various inhibitors (ROSCO Diagnostica A/S), chromogenic medium for the detection of ESBL/carbapenemase-producing Enterobacteriaceae (CPE) isolates, and the VITEK 2 Compact system (BioMerieux).

RESULTS

944 isolates of K. pneumoniae were detected in various clinical specimens. Among these, ESBL-producing strains were detected in 349/944 (37%), whereas carbapenem- resistant strains in 188/944 (20%) of the isolates. The remaining isolates (407/944 [43%]) belonged to the wild type. ESBL isolates were the most common in wound swabs (138 [39.5%]), whereas CRKP isolates in screening samples (110 [58.5%]). The majority of ESBL isolates were detected in surgical departments (105 [30.1%]), whereas CRKP isolates in adult intensive care unit departments (79 [42.%]).

CONCLUSION

Our results show an increasing frequency of CRKP strains. This presents a significant issue in terms of infection prevention and control in hospital settings.

Correlation of CRISPR/Cas and Antimicrobial Resistance in Klebsiella pneumoniae Clinical Isolates Recovered from Patients in Egypt Compared to Global Strains

The CRISPR/Cas system has been long known to interfere with the acquisition of foreign genetic elements and was recommended as a tool for fighting antimicrobial resistance. The current study aimed to explore the prevalence of the CRISPR/Cas system in Klebsiella pneumoniae isolates recovered from patients in Egypt in comparison to global strains and correlate the CRISPR/Cas to susceptibility to antimicrobial agents. A total of 181 clinical isolates were PCR-screened for cas and selected antimicrobial resistance genes (ARGs). In parallel, 888 complete genome sequences were retrieved from the NCBI database for in silico analysis. CRISPR/Cas was found in 46 (25.4%) isolates, comprising 18.8% type I-E and 6.6% type I-E*. Multidrug resistance (MDR) and extensive drug resistance (XDR) were found in 73.5% and 25.4% of the isolates, respectively. More than 95% of the CRISPR/Cas-bearing isolates were MDR (65.2%) or XDR (32.6%). No significant difference was found in the susceptibility to the tested antimicrobial agents among the CRISPR/Cas-positive and -negative isolates. The same finding was obtained for the majority of the screened ARGs. Among the published genomes, 23.2% carried CRISPR/Cas, with a higher share of I-E* (12.8%). They were confined to specific sequence types (STs), most commonly ST147, ST23, ST15, and ST14. More plasmids and ARGs were carried by the CRISPR/Cas-negative group than others, but their distribution in the two groups was not significantly different. The prevalence of some ARGs, such as blaKPC, blaTEM, and rmtB, was significantly higher among the genomes of the CRISPR/Cas-negative strains. A weak, nonsignificant positive correlation was found between the number of spacers and the number of resistance plasmids and ARGs. In conclusion, the correlation between CRISPR/Cas and susceptibility to antimicrobial agents or bearing resistance plasmids and ARGs was found to be nonsignificant. Plasmid-targeting spacers might not be naturally captured by CRISPR/Cas. Spacer match analysis is recommended to provide a clearer image of the exact behavior of CRISPR/Cas towards resistance plasmids.

The Presence of Virulent and Multidrug-Resistant Clones of Carbapenem-Resistant Klebsiella pneumoniae in Southeastern Brazil

The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) represents an urgent threat to global public health due to the limited therapeutic options available to control this pathogen. This study aims to analyze the molecular epidemiology, antimicrobial resistance and virulence profile of CRKP isolated from patients at hospitals in Southeastern Brazil. KPC and other beta-lactamase genes were detected in all strains, which were also multidrug-resistant (MDR). In addition, 11 strains showed resistance to last-resort antimicrobials, such as colistin and tigecycline. MLST analysis revealed eight different sequence types (ST11, ST37, ST147, ST340, ST384, ST394, ST437, and ST628), being two (ST628 and ST394) reported for the first time in Brazil. Strains belonging to the clonal complex 258 (CC258) "high-risk clones" were prevalent in this study. The Galleria mellonella model showed the emergence of virulent CRKP strains in the healthcare environment and, suggests that colistin-resistant strains were associated with higher virulence. This study shows the presence of virulent CRKP-MDR strains in hospitals across Southeastern Brazil, and draws attention to the presence of highly virulent emerging CRKP-MDR ST628 strains, showing that virulent and resistant clones can emerge quickly, requiring constant monitoring.

High frequency of NDM-1 and OXA-48 carbapenemase genes among Klebsiella pneumoniae isolates in central Iran

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_TEM (77/77; 100%), bla_CTX-M1 (76/77; 98.7%), bla_SHV (76/77; 98.7%), bla_CTX-M15 (73/77; 94.8%) for ESBL; bla_CIT 28 (48.3%) and bla_CMY-2 26 (44.8%) for AMPC β-lactamase; and bla_OXA-48 46 (90.1%) and bla_NDM 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.

High Prevalence of blaNDM Among Carbapenem Non-Susceptible Klebsiella pneumoniae in a Tunisian Hospital First Report of blaNDM-9, blaKPC-20, and blaKPC-26 Genes

Fifty-four carbapenem non-susceptible Klebsiella pneumoniae (CNSKP) isolates were collected from a Tunisian hospital over a period of 13 consecutive months. Carbapenemase production and the prevalence of carbapenemase-encoding genes were investigated using combined-disk test (CDT), modified Carba NP (mCarba NP) test, and UV-spectrophotometry method complemented by PCR experiments and sequencing. Carbapenemase production was detected by the mCarba NP test and CDT in 92.59% and 96.29% of the 54 CNSKP isolates, respectively; while imipenem hydrolysis was detected using UV-spectrophotometry in the crude extracts of 44 isolates. bla_NDM, bla_OXA-48-like, and bla_KPC carbapenemase-encoding genes were found in 48, 31, and 22 isolates, respectively. Remarkably, bla_NDM-9, bla_KPC-20, and bla_KPC-26 genes were reported. The co-occurrence of carbapenemase-encoding genes in a single isolate was detected in 62.96% of the isolates. The analysis of clonal relationships between the isolates by pulsed field gel electrophoresis revealed that the majority of them were genetically unrelated. Our investigation provides molecular data on enzymatic mechanism of carbapenem non-susceptibility among 54 CNSKP showing the dominance of bla_NDM, and comprises the first identification of bla_NDM-9, bla_KPC-20, and bla_KPC-26 genes in a Tunisia hospital.

Molecular characterization of class 1 integrons in carbapenem-resistant Enterobacterales isolates

OBJECTIVE

Carbapenem-resistant Enterobacterales (CRE) infections result in higher treatment costs and mortality rates. Integrons play important roles in emergence and spread of antibiotic resistant genes. To get a better understand on the effects of integron on CRE resistance, distribution of common carbapenemase genes and class 1 integron in clinical CRE isolates were investigated.

METHOD

Carbapenemase genes, including bla_KPC, bla_VIM, bla_IMP, bla_NDM, bla_GES, bla_VEB and bla_OXA-23, were screened in 161 CRE isolates and subtypes of these genes were confirmed through sequence analysis. Class 1 integron was screened and common promoter and gene cassette arrays were determined by sequencing. The resistant rates to clinical commonly used antibiotics between integron positive and integron negative CRE isolates were compared.

RESULTS

Of 161 CRE isolates, the most prevalent carbapenemase gene was bla_KPC-2, which was detected in 139 isolates, including 99 Klebsiella pneumoniae. Class 1 integron was detected in 78 isolates. Twenty different gene cassettes, including two carbapenemase genes bla_VEB-1 and bla_IMP-4, and nine different gene cassette arrays, including bla_VEB-1-aadB-arr-2-cmlA5-bla_OXA-10-aadA1, aadB-catB8-bla_OXA-10-aadA1-dfrA1-aacA4 and bla_IMP-4-qacG-aacA4-catB3, were detected. Five types of common promoters were identified. Relative weak promoter PcH1 was the dominant type. Resistant rates of CRE isolates containing class 1 integrons to ceftazidime, amikacin, trimethoprim/sulfamethoxazole and gentamicin were higher than those without class 1 integrons (P < 0.05).

CONCLUSION

Class 1 integrons play important roles in the emergence and spread of CRE resistance. To the best of our knowledge, this is the first report of aadB-catB8-bla_OXA-10-aadA1-dfrA1-aacA4 and bla_IMP-4-qacG-aacA4-catB3 in the same Providencia rettgeri isolate and bla_VEB-1-aadB-arr-2-cmlA5-bla_OXA-10-aadA1 in P. rettgeri.

Systematic Review and Meta-analysis on Extended-Spectrum β-lactamases Producing Klebsiella pneumoniae in Nepal

Objective

This systematic review and meta-analysis aimed to assess the pool estimates of extended-spectrum β-lactamases producing K. pneumoniae (ESBL-KP) and study their drug resistance profile by evaluating the studies from Nepal.

Methods

A literature search was carried out in PubMed, Google Scholar, and NepJOL to screen all articles on ESBL-KP published between 2011 and 2021 from Nepal. This review was conducted following Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. Relevant data were extracted, and R language 4.2.0 software was used for statistical analysis.

Results

The pooled prevalence of K. pneumoniae was 5%, while the pooled prevalence of ESBL and multidrug resistance (MDR) in K. pneumoniae were 23% and 55%, respectively. Imipenem was the drug of choice (in vitro) against ESBL-KP infection.

Conclusion

Our analyses showed a high prevalence of ESBL-KP and their high resistance toward commonly used drugs. This study highlights the need for the development of new antibiotics for the management of ESBL-KP infections.

Genotypic Characterization of Carbapenem-Resistant Klebsiella pneumoniae Isolated from an Egyptian University Hospital

Globally, Klebsiella pneumoniae (K. pneumoniae) has been identified as a serious source of infections. The objectives of our study were to investigate the prevalence of multidrug-resistant (MDR) K. pneumoniae in Tanta University Hospitals, Gharbia Governorate, Egypt; characterize their carbapenem resistance profiles; and identify their different capsular serotypes. We identified and isolated 160 (32%) K. pneumoniae from 500 different clinical samples, performed antimicrobial susceptibility testing, and then used multiplex PCR to detect carbapenemase genes and capsular serotypes K1, K2, K3, K5, K20, K54, and K57. We detected phenotypic carbapenem resistance in 31.3% (50/160) of the isolates; however, molecular assays revealed that 38.75% (62/160) of isolates were carrying carbapenemase-encoding genes. Generally, blaOXA-48 was the prevalent gene (15.5%), followed by blaVIM (15%), blaIMP (7.5%), blaKPC (4%), and blaNDM (3.8%). BlaVIM and blaOXA-48 correlated with phenotypic resistance in 91.67% and 88% of the isolates that harbored them, respectively. Capsular typing showed that the most prevalent pathotype was K1 (30.6%), followed by K57 (24.2%), K54 (19.35%), K20 (9.67%), and K2 (6.45%). A critical risk to community health is posed by the high incidence of multidrug-resistant (MDR) virulent K. pneumoniae isolates from our hospital, and our study examines this pathogen's public health and epidemiological risks.

New advances in management and treatment of multidrug-resistant Klebsiella pneumoniae

INTRODUCTION

The management of multidrug-resistant (MDR) Klebsiella pneumoniae (KP) represents a major challenge in the field of infectious diseases. It is associated with a high rate of nosocomial infections with a mortality rate that reaches approximately 50%, even when using an effective antimicrobial therapy. Therefore, combined actions addressing infection control and antibiotic stewardship are required to delay the emergence of resistance. Since new antimicrobial agents targeting MDR-GNB bacteria have been produced during the last years and are now available for physicians to treat MDR, it is fundamental to choose appropriate antimicrobial therapy for K. pneumoniae infection.

AREAS COVERED

The PubMed database was searched to review the most significant recent literature on the topic, including data from articles coming from endemic areas and from the current European and American Guidelines.

EXPERT OPINION

We explore the most effective strategies for prevention of MDR-KP spread and the currently available treatment options, focusing on comparing old strategies and new compounds. We reviewed data concerning newly developed drugs that could play an important role in the future; we also propose a treatment algorithm that could be useful for physicians in daily clinical practice.

Class 1 integrons and multiple mobile genetic elements in clinical isolates of the Klebsiella pneumoniae complex from a tertiary hospital in eastern China

Background

The emergence of highly drug-resistant K. pneumoniae, has become a major public health challenge. In this work, we aim to investigate the diversity of species and sequence types (STs) of clinical Klebsiella isolates and to characterize the prevalence and structure of class 1 integrons.

Methods

Based on the whole genome sequencing, species identification was performed by 16S rRNA gene homology and average nucleotide identity (ANI) analysis. STs were determined in accordance with the international MLST schemes for K. pneumoniae and K. variicola. Integron characterization and comparative genomic analysis were performed using various bioinformatic tools.

Results

Species identification showed that the 167 isolates belonged to four species: K. pneumoniae, K. variicola subsp. variicola, K. quasipneumoniae and K. aerogenes. Thirty-six known and 5 novel STs were identified in K. pneumoniae, and 10 novel STs were identified in K. variicola subsp. variicola. Class 1 integrons were found in 57.49% (96/167) of the isolates, and a total of 169 resistance gene cassettes encoding 19 types of resistance genes, including carbapenem resistance gene (bla _IPM-4) and class D β-lactamases gene (bla _OXA-1 and bla _OXA-10), were identified. Among the 17 complete genomes, 29 class 1 integrons from 12 groups were found, only 1 group was encoded on chromosomes. Interestingly, one plasmid (pKP167-261) carrying two copies of approximately 19-kb IS26-Int1 complex resistance region that contains an integron and a multidrug resistance gene fragment.

Conclusion

The results of this work demonstrated that the species and STs of the clinical Klebsiella isolates were more complex by the whole genome sequence analysis than by the traditional laboratory methods. Finding of the new structure of MGEs related to the resistance genes indicates the great importance of deeply exploring the molecular mechanisms of bacterial multidrug resistance.

Antimicrobial Resistance and Molecular Characterization of Gene Cassettes from class 1 Integrons in Carbapenem-resistant Escherichia coli strains

OBJECTIVE

To investigate the distribution of class 1 integrons and their variable regional molecular characteristics, as well as the diversity of promoter and drug sensitivity of CR-Eco (carbapenem-resistant E. coli) strains.

METHOD

A total of 117 CR-Eco strains, collected between 2012.01 and 2019.12, underwent fully automated bacterial identification and sensitization using VITEK-2 Compact and supplemented by K-B assay. PCR was employed to screen for class 1 integrase genes and integron variable regions, while the promoter type and variable region gene cassette characteristics were determined by sequencing analysis.

RESULTS

The positive rate of the class 1 integron of the CR-Eco strains was 83.70% (92/117) herein. Moreover, class 1 integrase-positive strains exhibited statistically significant resistance to aztreonam, ceftazidime, ciprofloxacin, ceftriaxone, gentamicin, meropenem, and trimethoprim-sulfamethoxazole compared to integron-negative strains (P < 0.05). Variable regions were observed in 77 of the 92 class 1 integrase-positive strains. In addition, seven gene cassettes were detected, namely dfrA17-aadA5, aadA22, dfrA12-aadA2, dfrA12, dfrA17, dfrA27 and aadA. Finally, five types of class 1 integron variable region promoters were identified in those 77 strains, including PcW, PcH1, PcW_TGN-10, PcH1_TGN-10, and P2, which were detected in 48, 18, 8, 2, and 1 strains, respectively.

CONCLUSION

The primary integrator variable region gene cassettes of this class were dfrA and aadA. The integron-positive strains displayed simultaneous high resistance to multiple antimicrobial drugs. The integrator variable region promoters of the CR-Eco strains are primarily weak and can potentially form and spread drug resistance.

Early Response of Antimicrobial Resistance and Virulence Genes Expression in Classical, Hypervirulent, and Hybrid hvKp-MDR Klebsiella pneumoniae on Antimicrobial Stress

Klebsiella pneumoniae is an increasingly important hospital pathogen. Classical K. pneumoniae (cKp) and hypervirulent K. pneumoniae (hvKp) are two distinct evolutionary genetic lines. The recently ongoing evolution of K. pneumoniae resulted in the generation of hybrid hvKP-MDR strains. K. pneumoniae distinct isolates (n = 70) belonged to 20 sequence types with the prevalence of ST395 (27.1%), ST23 (18.6%), ST147 (15.7%), and ST86 (7.1%), and 17 capsular types with the predominance of K2 (31.4%), K57 (18.6%), K64 (10.0%), K1 (5.7%) were isolated from patients of the Moscow neurosurgery ICU in 2014-2019. The rate of multi-drug resistant (MDR) and carbapenem-resistant phenotypes were 84.3% and 45.7%, respectively. Whole-genome sequencing of five selected strains belonging to cKp (ST395^K47 and ST147^K64), hvKp (ST86^K2), and hvKp-MDR (ST23^K1 and ST23^K57) revealed bla_SHV, bla_TEM, bla_CTX, bla_OXA-48, and bla_NDM beta-lactamase genes; acr, oqx, kpn, kde, and kex efflux genes; and K. pneumoniae virulence genes. Selective pressure of 100 mg/L ampicillin or 10 mg/L ceftriaxone induced changes of expression levels for named genes in the strains belonging to cKp, hvKp, and hybrid hvKp-MDR. Obtained results seem to be important for epidemiologists and clinicians for enhancing knowledge about hospital pathogens.