Co-existence of NDM-1 and OXA-48 genes in Carbapenem Resistant Klebsiella pneumoniae clinical isolates in Kafrelsheikh, Egypt

The Increased Prevalence of rmpA Gene in Klebsiella pneumoniae Isolates Coharboring blaNDM and blaOXA-48-like Genes

The emergence of carbapenemase-producing Klebsiella pneumoniae poses a substantial risk to public health. It is essential to comprehend the influence of carbapenemase on the virulence characteristics of K. pneumoniae in order to devise successful strategies for combating these infections. In this study, we explored the distribution disparity of virulence determinants between carbapenemase-producing (CP-Kp, n = 52) and carbapenemase-nonproducing (CN-Kp, n = 43) isolates. The presence of carbapenemases was detected via the modified carbapenem inactivation method and confirmed by PCR. The New Delhi metallo-β-lactamase (blaNDM) and Oxacillinase-48-like (blaOXA-48-like) genes were the most prevalent (94.23% and 76.92%, respectively) in CP-Kp isolates. Coexistence of blaNDM and blaOXA-48-like was observed in 71.15% of isolates, whereas 5.77% coharbored blaNDM and blaKPC. PCR analysis revealed the presence of several virulence genes, including adhesins (fimH, 92.63%, mrkD, 97.89%), capsule-associated virulence (uge, 90.53%), the K2 capsule serotype (k2, 6.32%), the iron acquisition system (kfu, 23.16%), and the regulator of mucoid phenotype (rmpA, 28.42%). A significantly higher prevalence of rmpA was detected in the CP-Kp compared with the CN-Kp (24/52 vs. 3/43, p < 0.0001), indicating a potential association between rmpA and carbapenemase acquisition. In addition, the majority of rmpA (22/24) positive isolates in the CP-Kp isolates coharbored blaNDM and either blaOXA-48-like or blaKPC.

Genomic analysis of extensively drug resistant (XDR) Klebsiella pneumoniae high-risk clone ST14 co-harboring blaNDM and blaOXA-48 recovered from Saudi Arabia

BACKGROUND

This study presents a comprehensive genomic analysis of NDM and OXA-48-producing Klebsiella pneumoniae in the Western region of Saudi Arabia, traversed by tens of millions of Muslims from various countries annually. This significant influx of visitors invariably leads to the spread and diversity of MDR bacteria.

METHODS

Genome sequencing was performed using MiSeq system of 29 CPKP isolates that were NDM and OXA-48-positive isolated from nosocomial infections and demonstrated resistance to most antibiotics, including carbapenems.

RESULTS

WGS analysis showed that 12 (41.3%) isolates co-harbored blaOXA-48,blaCTX-M-15 and blaNDM genes. Notably, 16 (55.1%) isolates were identified as high-risk clone ST14, with 50% of these isolates co-harbored blaOXA-48, blaNDM and blaCTX-M-15 genes. All ST14 isolates were identified as capsular genotype KL2 and O1/O2v1 antigen with yersiniabactin locus ypt 14 carried by ICEKp5. The two isolates were identified as ST2096/KL64 hypervirulent K. pneumoniae (hvKp) clone harboring several virulence factors, including the regulator of the mucoid phenotype rmpA2 and aerobactin (iuc-1). Interestingly, two of the hvKp ST383/KL30 isolates were resistant to all tested antimicrobials except colistin and tigecycline, and simultaneously carried numerous ESBLs and carbapenemase genes. These isolates also harbor several virulence factors such as rmpA1, rmpA2, carried on KpVP-1, and aerobactin (iuc-1).

CONCLUSION

this study provides insights into the spread and prevalence of high-risk clones of CPKP in the Western region of Saudi Arabia. The ST14 high-risk clone appears to be the predominant CPKP clone in this region, posing a significant threat to public health. This study also reports the presence of two globally disseminated hypervirulent K. pneumoniae (hvKp) clones, namely ST2096 and ST383. Therefore, it is essential to improve surveillance and implement strict infection control measures in this region, which receives a substantial number of visitors to effectively monitor and reduce the spread of high-risk clones of antimicrobial-resistant bacteria, including CPKP.

The Importance of Carbapenemase-Producing Enterobacterales in African Countries: Evolution and Current Burden

Antimicrobial resistance (AMR) is a worldwide healthcare problem. Multidrug-resistant organisms (MDROs) can spread quickly owing to their resistance mechanisms. Although colonized individuals are crucial for MDRO dissemination, colonizing microbes can lead to symptomatic infections in carriers. Carbapenemase-producing Enterobacterales (CPE) are among the most important MDROs involved in colonizations and infections with severe outcomes. This review aimed to track down the first reports of CPE in Africa, describe their dissemination throughout African countries and summarize the current status of CRE and CPE data, highlighting current knowledge and limitations of reported data. Two database queries were undertaken using Medical Subject Headings (MeSH), employing relevant keywords to identify articles that had as their topics beta-lactamases, carbapenemases and carbapenem resistance pertaining to Africa or African regions and countries. The first information on CPE could be traced back to the mid-2000s, but data for many African countries were established after 2015-2018. Information is presented chronologically for each country. Although no clear conclusions could be drawn for some countries, it was observed that CPE infections and colonizations are present in most African countries and that carbapenem-resistance levels are rising. The most common CPE involved are Klebsiella pneumoniae and Escherichia coli, and the most prevalent carbapenemases are NDM-type and OXA-48-type enzymes. Prophylactic measures, such as screening, are required to combat this phenomenon.

Investigating the relationship between carbapenemase production and biofilm formation in Klebsiella pneumoniae clinical isolates

OBJECTIVE

Carbapenemase production and biofilm formation in K. pneumoniae are crucial factors influencing the pathogenicity and antibiotic resistance of this bacterium. This study investigated the interplay between carbapenemase production and biofilm formation in K. pneumoniae clinical isolates.

RESULTS

The distribution of biofilm-forming ability significantly differed between carbapenemase-producing (CP-Kp) (n = 52) isolates and carbapenemase-nonproducing (CN-Kp) isolates (n = 37), suggesting a potential link between carbapenemase production and biofilm formation. All the blaNDM-1-harbouring isolates demonstrated biofilm formation, with varying levels classified as strong (33.33%), moderate (22.22%), or weak (44.45%). blaNDM-1 and blaKPC-coharbouring isolates did not exhibit strong or moderate biofilm formation. blaNDM-1 and blaOXA-48-coharbouring isolates were predominantly moderate (48.65%), followed by weak (32.43%), with none showing strong biofilm production. These findings suggest a correlation between the presence of carbapenemases and biofilm-forming ability; however, the heterogeneity in biofilm-forming abilities associated with different carbapenemase types and the absence of strong biofilm producers in the detected carbapenemase combinations prompt a closer look at the complex regulatory mechanisms governing biofilm formation in CP-Kp isolates.

Distribution of ß-Lactamase Genes Among Multidrug-Resistant and Extended-Spectrum ß-Lactamase-Producing Diarrheagenic Escherichia coli from Under-Five Children in Ethiopia

Purpose

Escherichia coli strains that produce extended-spectrum ß-lactamase (ESBL) and carbapenemase are among the major threats to global health. The objective of the present study was to determine the distribution of ß-lactamase genes among multidrug-resistant (MDR) and ESBL-producing Diarrheagenic E. coli (DEC) pathotypes isolated from under-five children in Ethiopia.

Patients and Methods

A cross-sectional study was conducted in Addis Ababa and Debre Berhan, Ethiopia. It was a health-facility-based study and conducted between December 2020 and August 2021. A total of 476 under-five children participated in the study. DEC pathotypes were detected by conventional Polymerase Chain Reaction (PCR) assay. After evaluating the antimicrobial susceptibility profile of the DEC strains by disk diffusion method, confirmation test was done for ESBL and carbapenemase production. ß-lactamase encoding genes were identified from phenotypically ESBLs and carbapenemase positive DEC strains using PCR assay.

Results

In total, 183 DEC pathotypes were isolated from the 476 under-five children. Seventy-nine (43%, 79/183) MDR-DEC pathotypes were identified. MDR was common among enteroaggregative E. coli (EAEC) (58%, 44/76), followed by enterotoxigenic E. coli (ETEC) (44%, 17/39)) and enteroinvasive E. coli (EIEC) (30%, 7/23). Phenotypically, a total of 30 MDR-DEC pathotypes (16.4%, 30/183) were tested positive for ESBLs. Few ETEC (5.1%, 2/39) and EAEC (2.6%, 2/76) were carbapenemase producers. The predominant β-lactamase genes identified was blaTEM (80%, 24/30) followed by blaCTX-M (73%, 22/30), blaSHV (60%, 18/30), blaNDM (13%, 4/30), and blaOXA-48 (13%, 4/30). Majority of the ß-lactamase encoding genes were detected in EAEC (50%) and ETEC (20%). Co-existence of different β-lactamase genes was found in the present study.

Conclusion

The blaTEM, blaCTX-M, blaSHV, blaNDM, and blaOXA-48, that are associated with serious and urgent threats globally, were detected in diarrheagenic E. coli isolates from under-five children in Ethiopia. This study also revealed the coexistence of the β-lactamase genes.

Beta-lactam Resistance Profile among Klebsiella pneumoniae Clinical Isolates from Alexandria, Egypt

Klebsiella pneumoniae is a major drug-resistant human pathogen accountable for a wide range of infections. In this cross-sectional study, we aimed to determine the phenotypic and genotypic features of β-lactamase-producing K. pneumoniae clinical isolates from Alexandria, Egypt. A total of 50 nonduplicated clinical isolates of K. pneumoniae were obtained from various specimens. They were identified biochemically and by biotyping using mass spectrometry. For molecular characterization, plasmid profile analysis was performed. Screening for extended spectrum β-lactamases (ESBLs), carbapenemases and AmpC production was carried out phenotypically and genotypically. Correlation analysis was performed to assess the relationship between phenotype, genotype and resistance patterns among the studied isolates. The dendrogram demonstrated 38 distinct plasmid profiles among 62% of our isolates. According to antimicrobial susceptibility testing, 90% of isolates were multi/extensive-drug resistant. Nineteen out of 50 (38%) were resistant to cefoxitin, while only 10 (20%) were resistant to imipenem. All isolates were susceptible to colistin. Phenotypically, ESBL producers (78%) were the most common, followed by carbapenemase producers (24%). Genotypically, the most common ESBL gene was blaSHV (90%), followed by blaCTX-Mu (74%), while the most common carbapenemase genes were blaNDM (56%) and blaOXA-48 (54%). No blaKPC or blaIMP were detected. Plasmid-mediated AmpC resistance was confirmed in only two out of 19 cefoxitin-resistant isolates. Both the blaNDM and blaOXA.48 genes were significantly positive correlated (rho = 0.56, p = 0.004). Absence of blaKPC among carbapenem resistant K. pneumoniae isolates in Alexandria, Egypt. AmpC production is not the main factor behind the resistance to cefoxitin among our isolates.

Characterization of Carbapenem-Resistant K. Pneumoniae Isolated from Intensive Care Units of Zagazig University Hospitals

The advent of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant challenge to public health, as carbapenems are typically employed as a last resort to treat nosocomial infections caused by such organisms, especially in intensive care units (ICUs). This study aims to characterize the CRKP isolated from patients admitted to the Zagazig University Hospitals (ZUHs) ICU in Egypt. About 56.2%, 41.0%, and 32.4% of the isolates indicated the presence of bla_NDM, bla_OXA-48, and bla_KPC, respectively. Carbapenemase-encoding genes were found in many isolates, and bla_NDM was the most predominant gene. Nevertheless, this situation has become a heavy burden in developing countries, including Egypt, and is associated with substantial morbidity, mortality, and increased healthcare expenses.

Carbapenem-Resistant Klebsiella pneumoniae Among Patients with Ventilator-Associated Pneumonia: Evaluation of Antibiotic Combinations and Susceptibility to New Antibiotics

Background

Carbapenemase-producing Gram-negative bacteria, particularly Klebsiella pneumoniae (K. pneumoniae), are at the forefront of the list of causative agents of ventilator-associated pneumonia (VAP). The treatment options for such infections are limited, and various antimicrobial combinations have been suggested as alternatives in clinical practice. New antibiotics, such as ceftazidime/avibactam, ceftolozane/tazobactam and cefiderocol, have shown advantages in both in vitro and clinical studies.

Purpose

To evaluate the in vitro effect of meropenem–ciprofloxacin and meropenem–colistin combinations on carbapenem-resistant (CR) K. pneumoniae VAP isolates and to determine their susceptibility to new antibiotics.

Methods

Seventy-three K. pneumoniae isolates from 176 endotracheal samples from VAP cases were studied. Antibiotic susceptibility testing and phenotypic detection of extended-spectrum β lactamase (ESBL) and carbapenemase production were done. CR K. pneumoniae isolates were tested for the five predominant carbapenemase genes (bla_KPC, bla_OXA-48, bla_NDM,bla_VIM, and bla_IMP). In vitro evaluation of meropenem–ciprofloxacin and meropenem–colistin combinations was done by MIC test strips. Susceptibility to new antibiotics was tested by disk diffusion method.

Results

Sixty-three (86.3%) of the isolates were ESBL producers and 52 (71.2%) were carbapenem resistant. Bla_NDM was the most prevalent carbapenemase gene (50%), followed by bla_OXA-48, (36.5%) then bla_KPC in (11.5%). Bla_VIM and bla_IMP were not detected. Meropenem–ciprofloxacin combination showed indifferent effect on all isolates, while meropenem–colistin combination showed 25% synergism, 15.4% addition and 59.6% indifference. All (100%) CR K. pneumoniae isolates were resistant to ceftolozane/tazobactam and 79% were resistant to ceftazidime/avibactam, while 96% were sensitive to cefiderocol.

Conclusion

A high rate of carbapenem resistance exists among VAP K. pneumoniae isolates. Meropenem–colistin combination and cefiderocol appear to be potential treatment options for infections caused by CR K. pneumoniae. Resistance to the tested new β-lactam/β-lactamase inhibitors was high, signifying a major threat.

Co-occurrence of genes encoding carbapenemase, ESBL, pAmpC, and Non-β-Lactam resistance among Klebsiella pneumonia and E. coli clinical isolates in Tunisia

This study aimed to investigate the molecular mechanisms of carbapenem and colistin resistance in K. pneumoniae and E. coli isolates obtained from hospitalized patients in Carthagene International Hospital of Tunis. A total of 25 K. pneumoniae and 2 E. coli clinical isolates with reduced susceptibility to carbapenems were recovered. Susceptibility testing and phenotypic screening tests were carried out. ESBL, AmpC, carbapenemase, and other antibiotic resistance genes were sought by PCR-sequencing. The presence of plasmid-mediated colistin resistance genes (mcr-1-8) was examined by PCR and the nucleotide sequence of the mgrB gene was determined. The analysis of plasmid content was performed by PCR-Based Replicon Typing (PBRT). The clonality of isolates was assessed by PFGE and multilocus sequence typing (MLST). All of the isolates produced carbapenemase activity. They showed a great variation in the distribution of ESBL, AmpC, carbapenemase, and other plasmid-mediated resistance determinants. K. pneumoniae isolates carried bla_NDM-1 (n=11), bla_OXA-48 (n=11), bla_NDM-1 + bla_OXA-48 (n=1), bla_NDM-1 + bla_VIM-1 (n=1), bla_OXA-204 (n=1), along with bla_CTX-M , bla_OXA , bla_TEM , bla_CMY , bla_DHA and bla_SHV genes variants on conjugative plasmid of IncL/M, IncR, IncFII_K , IncFIB, and IncHI1 types. Three sequence types ST101, ST307, and ST15 were identified. The mgrB alteration g109a (G37S) was detected in a single colistin-resistant, NDM-1 and OXA-48-coproducing K. pneumoniae isolate. The two E. coli isolates belonged to ST95, co-produced NDM-1 and CTX-M-15, and harbored plasmid of IncFII and IncFIB types. To our knowledge, this is the first report in Tunisia of NDM-1, OXA-48, and CTX-M-15 coexistence in colistin-resistant K. pneumoniae ST15.

Characteristics of Carbapenem-Resistant Gram-Negative Bacilli in Patients with Ventilator-Associated Pneumonia

Carbapenem-resistant Gram-negative bacilli (CR-GNB) has become a global threat. In hospital settings, the association of CR-GNB with ventilator-associated pneumonia (VAP) is a critical public health concern owing to their high resistance rate to most antibiotics. The present study aims to identify the frequency of carbapenem-resistance and to determine the rate of multidrug resistance (MDR), extensive drug resistance (XDR) and pan-drug resistance (PDR) among CR-GNB infections in VAP. Antimicrobial susceptibility testing was carried out using the disk diffusion method and the detection of carbapenemases was screened using the imipenem-E test and the modified carbapenem-inactivation method (mCIM). The isolates were verified by polymerase chain reaction (PCR) for the presence of bla_NDM, bla_SPM, bla_VIM, bla_IMP and bla_GIM genes. 89.5%, 14%, 17.5%, 10.5%, 3.5% of isolates exhibited the presence of bla_NDM, bla_VIM, bla_SPM, bla_IMP and bla_GIM, respectively. 76%, 17% and 7% of isolates were PDR, XDR, and MDR, respectively. Carbapenem-resistance genes were identified in a significant percentage and bla_NDM was the most predominant gene. All isolates were highly resistant to most antibiotics. This health concern has proven to be a big challenge in developing countries such as Egypt, as it is associated with high morbidity, high mortality, and raised healthcare costs.

Comparative genome analysis of colistin-resistant OXA-48-producing Klebsiella pneumoniae clinical strains isolated from two Iranian hospitals

BACKGROUND

Carbapenemase-producing Klebsiella pneumoniae (CP-KP) is becoming extensively disseminated in Iranian medical centers. Colistin is among the few agents that retains its activity against CP-KP. However, the administration of colistin for treatment of carbapenem-resistant infections has increased resistance against this antibiotic. Therefore, the identification of genetic background of co-carbapenem, colistin-resistance K. pneumoniae (Co-CCRKp) is urgent for implementation of serious infection control strategies.

METHODS

Fourteen Co-CCRKp strains obtained from routine microbiological examinations were subjected to molecular analysis of antimicrobial resistance (AMR) using whole genome sequencing (WGS).

RESULTS

Nine of 14 K. pneumoniae strains belonged to sequence type (ST)-11 and 50% of the isolates had K-locus type 15. All strains carried blaOXA-48 except for P26. blaNDM-1 was detected in only two plasmids associated with P6 and P26 strains belonging to incompatibility (Inc) groups; IncFIB, IncHI1B and IncFII. No blaKPC, blaVIM and blaIMP were identified. Multi-drug resistant (MDR) conjugative plasmids were identified in strains P6, P31, P35, P38 and P40. MICcolistin of K. pneumoniae strains ranged from 4 to 32 µg/ml. Modification of PmrA, PmrB, PhoQ, RamA and CrrB regulators as well as MgrB was identified as the mechanism of colistin resistance in our isolates. Single amino acid polymorphysims (SAPs) in PhoQ (D150G) and PmrB (R256G) were identified in all strains except for P35 and P38. CrrB was absent in P37 and modified in P7 (A200E). Insertion of ISKpn72 (P32), establishment of stop codon (Q30*) (P35 and P38), nucleotides deletion (P37), and amino acid substitution at position 28 were identified in MgrB (P33 and P42). None of the isolates were positive for plasmid-mediated colistin resistance (mcr) genes. P35 and P38 strains carried iutA, iucD, iucC, iucB and iucA genes and are considered as MDR-hypervirulent strains. P6, P7 and P43 had ICEKp4 variant and ICEKp3 was identified in 78% of the strains with specific carriage in ST11.

CONCLUSION

In our study, different genetic modifications in chromosomal coding regions of some regulator genes resulted in phenotypic resistance to colistin. However, the extra-chromosomal colistin resistance through mcr genes was not detected. Continuous genomic investigations need to be conducted to accurately depict the status of colistin resistance in clinical settings.

Editorial: Infectious diseases and NCDs persist despite concerted effort

Nil.