Comparing conventional, biochemical and genotypic methods for accurate identification of Klebsiella pneumoniae in Sudan

Genetic Insights on Meropenem Resistance Concerning Klebsiella pneumoniae Clinical Isolates

The transferable genetic elements are associated with the dissemination of virulence determinants amongst Klebsiella pneumoniae. Thus, we assessed the correlated antimicrobial resistance in carbapenem-resistant Klebsiella pneumoniae clinical isolates. Each isolate's ability to biosynthesize biofilm, carbapenemase, and extended-spectrum β-lactamase were examined. Genotypically, the biofilm-, outer membrane porin-, and some plasmid-correlated antimicrobial resistance genes were screened. About 50% of the isolates were multidrug-resistant while 98.4% were extended-spectrum β-lactamase producers and 89.3% were carbapenem-resistant. Unfortunately, 93.1% of the multidrug-resistant isolates produced different biofilm levels. Additionally, fimD and mrkD genes encoding adhesins were detected in 100% and 55.2% of the tested isolates, respectively. Also, the blaKPC, blaOXA-48-like, and blaNDM-encoding carbapenemases were observed in 16.1%, 53.6%, and 55.4% of the tested isolates, respectively. Moreover, the blaSHV and blaCTX-M extended-spectrum β-lactamase-associated genes were detected at 95.2% and 61.3%, respectively. Furthermore, aac(3)IIa, qnrB, and tetB resistance-correlated genes were observed in 38.1%, 46%, and 7.9% of the tested isolates, respectively. Certainly, the tested antimicrobial resistance-encoding genes were concurrently observed in 3.2% of the tested isolates. These findings confirmed the elevated prevalence of various antimicrobial resistance-associated genes in Klebsiella pneumoniae. The concurrent transferring of plasmid-encoding antimicrobial resistance-related genes could be associated with the possible acquisition of multidrug-resistant Klebsiella pneumoniae phenotypes.

HPLC-PDA Analysis of Polyacetylene Glucosides from Launaea capitata and Their Antibacterial and Antibiofilm Properties against Klebsiella pneumoniae

Background/Objectives: Bacterial resistance and virulence are challenges in treating bacterial infections, especially in Klebsiella pneumoniae. Plants of the Launaea Cass. genus are used traditionally to address a variety of diseases, including infections, but the potential bioactive compounds are unknown. Our goals were to verify the potential contribution of two major polyacetylene glycosides isolated from our previous study, (3S,6E,12E)-6,12-tetradecadiene-8,10-diyne-1-ol 3-O-β-D-glucopyranoside (1) and bidensyneoside A (syn. gymnasterkoreaside A) [(3R,8E)-3-hydroxy-8-decene-4,6-diyn-1-yl β-D-glucopyranoside] (2), to the anti-infective properties of Launaea capitata and to develop a dependable HPLC method for their quantification; Methods: On a panel of K. pneumoniae clinical isolates, the antibacterial action of 1, 2, and the methanol extract of the whole L. capitata plant were evaluated by broth microdilution assay, while their antibiofilm action was evaluated by the crystal violet assay. qRT-PCR investigated luxS, mrkA, wzm, and wbbm genes that encode biofilm formation and quorum sensing (QS). The antibacterial activity of 1 was revealed by employing mice infection. Chromatographic separation was conducted using isocratic elution on a Hypersil BDS C18 column using a photodiode array (PDA) detector; Results: Compound 1 showed antibacterial activity with MIC values of 16-128 µg/mL. It remarkably reduced strong and moderate biofilm-forming bacterial isolates from 84.21% to 42.1% compared with the extract (68.42%) and 2 (78.95%). Compound 1 also downregulated the QS genes, luxS, mrkA, wzm, and wbbm, and exhibited in vivo antibacterial action through the enhancement of the histological construction of the liver and spleen, decreased TNF-α immunoreaction, bacterial burden, and the inflammatory mediators IL-1β and IL-6. A successful HPLC-PDA approach was developed to separate the binary mixture of 1 and 2 in less than 10 min with high sensitivity, with detection limits down to 0.518 and 0.095 µg/mL for 1 and 2, respectively; Conclusions: Compound 1 exhibited remarkable antibacterial and antibiofilm properties and may contribute to the anti-infectious traditional uses of L. capitata, meriting further clinical studies and serving as a reliable quality control biomarker for the plant.

Proteome analysis, genetic characterization, and antibiotic resistance patterns of Klebsiella pneumoniae clinical isolates

Klebsiella pneumoniae (K. pneumoniae) is a member of the ESKAPE group and is responsible for severe community and healthcare-associated infections. Certain Klebsiella species have very similar phenotypes, which presents a challenge in identifying K. pneumoniae. Multidrug-resistant K. pneumoniae is also a serious global problem that needs to be addressed. A total of 190 isolates were isolated from urine (n = 69), respiratory (n = 52), wound (n = 48) and blood (n = 21) samples collected from various hospitals in the Al-Qassim, Saudi Arabia, between March 2021 and October 2022. Our study aimed to rapidly and accurately detect K. pneumoniae using the Peptide Mass Fingerprinting (PMF) technique, confirmed by real-time PCR. Additionally, screening for antibiotic susceptibility and resistance was conducted. The primary methods for identifying K. pneumoniae isolates were culture, Gram staining, and the Vitek® 2 ID Compact system. An automated MALDI Biotyper (MBT) instrument was used for proteome identification, which was subsequently confirmed using SYBR green real-time polymerase chain reaction (real-time PCR) and microfluidic electrophoresis assays. Vitek® 2 AST-GN66 cards were utilized to evaluate the antimicrobial sensitivity of K. pneumoniae isolates. According to our results, Vitek® 2 Compact accurately identified 178 out of 190 (93.68%) K. pneumoniae isolates, while the PMF technique correctly detected 188 out of 190 (98.95%) isolates with a score value of 2.00 or higher. Principal component analysis was conducted using MBT Compass software to classify K. pneumoniae isolates based on their structure. Based on the analysis of the single peak intensities generated by MBT, the highest peak values were found at 3444, 5022, 5525, 6847, and 7537 m/z. K. pneumoniae gene testing confirmed the PMF results, with 90.53% detecting entrobactin, 70% detecting 16 S rRNA, and 32.63% detecting ferric iron uptake. The resistance of the K. pneumoniae isolates to antibiotics was as follows: 64.75% for cefazolin, 62.63% for trimethoprim/sulfamethoxazole, 59.45% for ampicillin, 58.42% for cefoxitin, 57.37% for ceftriaxone, 53.68% for cefepime, 52.11% for ampicillin-sulbactam, 50.53% for ceftazidime, 52.11% for ertapenem, and 49.47% for imipenem. Based on the results of the double-disk synergy test, 93 out of 190 (48.95%) K. pneumoniae isolates were extended-spectrum beta-lactamase. In conclusion, PMF is a powerful analytical technique used to identify K. pneumoniae isolates from clinical samples based on their proteomic characteristics. K. pneumoniae isolates have shown increasing resistance to antibiotics from different classes, including carbapenem, which poses a significant threat to human health as these infections may become difficult to treat.

Antibiotic Susceptibility, Biofilm-Forming Ability, and Prevalence of Extended-Spectrum Beta-Lactamase (ESBL)- and Biofilm-Associated Genes Among Klebsiella pneumoniae Isolates from Hospitalized Patients in Northwest of Iran

Klebsiella pneumoniae is an opportunistic bacterium, which is globally recognized for its high prevalence and antimicrobial resistance (AMR). Biofilm-forming capability, susceptibility testing, and phenotypic confirmatory test for extended-spectrum beta-lactamase (ESBL)-producing isolate recognition of 104 K. pneumoniae isolates were performed according to the Clinical Laboratory Standard Institute (CLSI) guidelines. The prevalence of ESBL-associated genes bla-VIM, bla-NDM, and bla-OXA-48, as well as biofilm-associated genes luxS, fimH1, wza, and mrkD, was determined by multiplex PCR. The highest resistance rate was against ampicillin (100.0%). Among the 104 K. pneumoniae isolates, 52 (50.0%) and 31 (29.8%) isolates were determined as multi- and extensively drug resistant (MDR, XDR), respectively. Moreover, 21 (40.4%) isolates were determined as ESBL producing. Among 50 biofilm-producing K. pneumoniae isolates, 7 (14.0%), 15 (30.0%), and 28 (56.0%) isolates exhibited high, moderate, and weak levels of biofilm formation, respectively. A number of 41 (78.8%) isolates were susceptible to colistin, and 10 (19.2%) were resistant. AMR was significantly higher (P < 0.05) in the biofilm-forming isolates compared with non-biofilm formers.

Klebsiella pneumonia in Sudan: Multidrug Resistance, Polyclonal Dissemination, and Virulence

The emergence and global expansion of hyper-virulent and multidrug resistant (MDR) Klebsiella pneumoniae is an increasing healthcare threat worldwide. The epidemiology of MDR K. pneumoniae is under-characterized in many parts of the world, particularly Africa. In this study, K. pneumoniae isolates from hospitals in Khartoum, Sudan, have been whole-genome sequenced to investigate their molecular epidemiology, virulence, and resistome profiles. Eighty-six K. pneumoniae were recovered from patients in five hospitals in Khartoum between 2016 and 2020. Antimicrobial susceptibility was performed by disk-diffusion and broth microdilution. All isolates underwent whole genome sequencing using Illumina MiSeq; cgMLST was determined using Ridom SeqSphere+, and 7-loci MLST virulence genes and resistomes were identified. MDR was observed at 80%, with 35 isolates (41%) confirmed carbapenem-resistant. Thirty-seven sequence types were identified, and 14 transmission clusters (TC). Five of these TCs involved more than one hospital. Ybt9 was the most common virulence gene detected, in addition to some isolates harbouring iuc and rmp1. There is a diverse population of K. pneumoniae in Khartoum hospitals, harbouring multiple resistance genes, including genes coding for ESBLs, carbapenemases, and aminoglycoside-modifying enzymes, across multiple ST's. The majority of isolates were singletons and transmissions were rare.

Characterization of Beta-Lactam Resistance Genes and Virulence Factors Associated with Multidrug-Resistant Klebsiella pneumoniae Isolated from Patients at Major Hospitals in Trinidad, West Indies

Accurate species identification and antibiotic resistance profiling are essential for the effective management of infections caused by bacterial pathogens. In this study, 373 clinical isolates of K. pneumoniae from major hospitals in Trinidad, West Indies, were characterized for resistance against beta-lactam antibiotics and the presence of genes encoding important virulence factors. Most of the isolates showed extended spectrum β-lactamase (ESBL) activity but few also displayed carbapenemase or 'ESBL + carbapenemase' activities. Polymerase chain reaction analysis revealed the presence of genes for ESBL subtypes bla_TEM, bla_SHV, and bla_CTX-M that were dominant in isolates with the ESBL phenotype as well as those that did not show ESBL or carbapenemase activities. The carbapenem resistance gene, bla_KPC, and the metallo-β-lactamase (MBL) gene, bla_NDM-1, were also detected in some of the isolates. Multiple virulence genes were also detected, but the fimH-uge was the most common combination found among the local isolates. The findings of this study represent the first comprehensive study on the prevalence of ESBL, KPC and MBL genes and virulence profiling in antibiotic-resistant K. pneumoniae in Trinidad. Furthermore, the occurrence of multiple resistant phenotypes and gene combinations were revealed, though at low prevalence rates. This work emphasizes the need to implement molecular-based techniques in diagnostic workflows for rapid and accurate species identification and profiling of resistance and virulence genes in K. pneumoniae in Trinidad and Tobago.

Biosensors for Klebsiella pneumoniae with Molecularly Imprinted Polymer (MIP) Technique

Nosocomial infection is one of the most important problems that occurs in hospitals, as it directly affects susceptible patients or patients with immune deficiency. Klebsiella pneumoniae (K. pneumoniae) is the most common cause of nosocomial infections in hospitals. K. pneumoniae can cause various diseases such as pneumonia, urinary tract infections, septicemias, and soft tissue infections, and it has also become highly resistant to antibiotics. The principal routes for the transmission of K. pneumoniae are via the gastrointestinal tract and the hands of hospital personnel via healthcare workers, patients, hospital equipment, and interventional procedures. These bacteria can spread rapidly in the hospital environment and tend to cause nosocomial outbreaks. In this research, we developed a MIP-based electrochemical biosensor to detect K. pneumoniae. Quantitative detection was performed using an electrochemical technique to measure the changes in electrical signals in different concentrations of K. pneumoniae ranging from 10 to 10⁵ CFU/mL. Our MIP-based K. pneumoniae sensor was found to achieve a high linear response, with an R² value of 0.9919. A sensitivity test was also performed on bacteria with a similar structure to that of K. pneumoniae. The sensitivity results show that the MIP-based K. pneumoniae biosensor with a gold electrode was the most sensitive, with a 7.51 (% relative current/log concentration) when compared with the MIP sensor applied with Pseudomonas aeruginosa and Enterococcus faecalis, where the sensitivity was 2.634 and 2.226, respectively. Our sensor was also able to achieve a limit of detection (LOD) of 0.012 CFU/mL and limit of quantitation (LOQ) of 1.61 CFU/mL.

Genomic Analysis of Multidrug-Resistant Hypervirulent (Hypermucoviscous) Klebsiella pneumoniae Strain Lacking the Hypermucoviscous Regulators (rmpA/rmpA2)

Hypervirulent K. pneumoniae (hvKP) strains possess distinct characteristics such as hypermucoviscosity, unique serotypes, and virulence factors associated with high pathogenicity. To better understand the genomic characteristics and virulence profile of the isolated hvKP strain, genomic data were compared to the genomes of the hypervirulent and typical K. pneumoniae strains. The K. pneumoniae strain was isolated from a patient with a recurrent urinary tract infection, and then the string test was used for the detection of the hypermucoviscosity phenotype. Whole-genome sequencing was conducted using Illumina, and bioinformatics analysis was performed for the prediction of the isolate resistome, virulome, and phylogenetic analysis. The isolate was identified as hypermucoviscous, type 2 (K2) capsular polysaccharide, ST14, and multidrug-resistant (MDR), showing resistance to ciprofloxacin, ceftazidime, cefotaxime, trimethoprim-sulfamethoxazole, cephalexin, and nitrofurantoin. The isolate possessed four antimicrobial resistance plasmids (pKPN3-307_type B, pECW602, pMDR, and p3K157) that carried antimicrobial resistance genes (ARGs) (bla_OXA-1,bla_CTX-M-15, sul2, APH(3″)-Ib, APH(6)-Id, and AAC(6′)-Ib-cr6). Moreover, two chromosomally mediated ARGs (fosA6 and SHV-28) were identified. Virulome prediction revealed the presence of 19 fimbrial proteins, one aerobactin (iutA) and two salmochelin (iroE and iroN). Four secretion systems (T6SS-I (13), T6SS-II (9), T6SS-III (12), and Sci-I T6SS (1)) were identified. Interestingly, the isolate lacked the known hypermucoviscous regulators (rmpA/rmpA2) but showed the presence of other RcsAB capsule regulators (rcsA and rcsB). This study documented the presence of a rare MDR hvKP with hypermucoviscous regulators and lacking the common capsule regulators, which needs more focus to highlight their epidemiological role.

A Comparison of Methods for Identifying Enterobacterales Isolates from Fish and Prawns

Enterobacterales is a prevalent order, which inhabits a variety of environments including food. Due to the high similarities between pathogenic and non-pathogenic species, their identification might be difficult and laborious, and therefore there is a need for rapid and precise identification. The aim of this study was to compare the effectiveness of the available methods of identifying order Enterobacterales strains isolated from fresh fish and shrimps (n = 62). The following methods were used in this study: biochemical, sequencing and identification using the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). For this purpose, biochemical identification was performed with the use of the EnteroTest 24N set, while the identification using the MALDI-TOF MS technology was operated on VITEK^® MS. Results were compared with identification made by 16S rRNA sequencing. The results of the study showed that conventional identification methods might provide a false result. Identification by VITEK^® MS to the species level was correct at 70.97%, and the accuracy of EnteroTest 24N identification did not exceed 50.0%. The genus identification reached 90.32% for the MALDI-TOF technique, while for EnteroTest 24N it was nearly 70.0%. Due to errors in identification, especially of pathogenic organisms, the use of each of these methods should be confirmed by another method, preferably sequencing.

Detection of mobile genetic elements in multidrug-resistant Klebsiella pneumoniae isolated from different infection sites in Hamadan, west of Iran

Objective

Klebsiella pneumoniae is one of most opportunistic pathogens that can be related to nosocomial infections. Increased acquisitions of multidrug resistance in this bacterium as well as the transfer of genes to other strains have caused concern. Integrons play key role in the acquisition and the spread of resistance genes. The aim of this study was evaluated the frequency of resistance genes sulI, sulII, tetA, tetB, class I (intI gene), class II integrons (intII gene) and the association between multidrug resistance and the presence of integrons in K. pneumoniae.

Results

Antibiotics susceptibility test was performed on 126 of K. pneumoniae isolates. Also, DNA extraction was done and genes were detected using PCR method. In this study, 67 isolates (53%), carrying both the sulI and sulII genes. Forty-five percent tetracycline-resistant isolates were tetA or tetB positive. The prevalence of intI gene was 96%, while only sixteen isolate harboring intII gene (12.5%). Our results showed the high prevalence of integrons in MDR K. pneumoniae, indicating the important role of these genes in the transmission of antibiotic resistance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-021-05748-9.

Molecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii From Khartoum State, Sudan

Carbapenem resistant Acinetobacter baumannii (CRAb) is an important global pathogen contributing to increased morbidity and mortality in hospitalized patients, due to limited alternative treatment options. Nine international clonal (IC) lineages have been identified in many countries worldwide, however, data still lacks from some parts of the world, particularly in Africa. We hereby present the molecular epidemiology of MDR A. baumannii from four hospitals in Khartoum, Sudan, collected from 2017 to 2018. Forty-two isolates were whole-genome sequenced, and subsequent molecular epidemiology was determined by core genome MLST (cgMLST), and their resistomes identified. All isolates had an array of diverse antibiotic resistance mechanisms conferring resistance to multiple classes of antibiotics. We found a predominance (88%) of IC2 (with the intrinsic OXA-66 and acquired OXA-23), and some with NDM-1. IC2 isolates were sub-divided into 4 STs separated by 5 to 431 allelic differences, and with evidence of seven transmission clusters. Isolates belonging to IC1, IC5, and IC9 were also identified. These data illustrate that MDR IC2 A. baumannii are widely distributed in Khartoum hospitals and are in possession of multiple antibiotic resistance determinants.

Diversity, Antibiotic Resistance, and Biofilm-Forming Ability of Enterobacteria Isolated from Red Meat and Poultry Preparations

A total of 44 samples of beef, pork, and poultry preparations were tested. Average counts (log cfu/g) of enterobacteria were 1.99 ± 0.99 (beef preparations), 1.96 ± 1.44 (pork), 2.09 ± 0.92 (chicken), and 2.17 ± 1.06 (turkey) (p > 0.05). Two hundred enterobacterial strains were identified and 13 genera (21 species) were distinguished, including species that are a significant cause of infection. The most common genera were Escherichia (32.5% of strains), Serratia (17.0%), Hafnia (12.5%), and Salmonella (12.0%). Isolates were screened by disc diffusion for susceptibility to 15 antibiotics. A total of 126 strains (63% of the isolates) were multirresistant (having resistance to two or more antibiotics), 46 (23%) were resistant to one antibiotic, and 28 (14%) were sensitive to all antibiotics. The average number of resistances per strain was 2.53 ± 2.05. A higher (p < 0.05) average number of resistances was observed in strains from turkey (3.14 ± 2.55) than in strains from beef (2.15 ± 1.22), pork (2.16 ± 1.39), or chicken (2.44 ± 2.22). At least 50% of strains showed resistance or reduced susceptibility to ampicillin, cefotaxime, ceftazidime, or streptomycin, considered to be "critically important" antimicrobial agents in human medicine. Seventy-nine strains (39.5%), 60 strains (30.0%), and 46 strains (23.0%) were weak, moderate, and strong biofilm producers (crystal violet assay), respectively. This investigation provides evidence that bacteria from red meat and poultry preparations pose major potential risk to consumers.