Epidemiology of resistance and phenotypic characterization of carbapenem resistance mechanisms in Klebsiella pneumoniae isolates at Sahloul University Hospital-Sousse, Tunisia

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.

The Global and Regional Prevalence of Hospital-Acquired Carbapenem-Resistant Klebsiella pneumoniae Infection: A Systematic Review and Meta-analysis

Background

Due to scarce therapeutic options, hospital-acquired infections caused by Klebsiella pneumoniae (KP), particularly carbapenem-resistant KP (CRKP), pose enormous threat to patients' health worldwide. This study aimed to characterize the epidemiology and risk factors of CRKP among nosocomial KP infections.

Method

MEDLINE, Embase, PubMed, and Google Scholar were searched for studies reporting CRKP prevalence from inception to 30 March 2023. Data from eligible publications were extracted and subjected to meta-analysis to obtain global, regional, and country-specific estimates. To determine the cause of heterogeneity among the selected studies, prespecified subgroup analyses and meta-regression were also performed. Odds ratios of CRKP-associated risk factors were pooled by a DerSimonian and Laird random-effects method.

Results

We retained 61 articles across 14 countries and territories. The global prevalence of CRKP among patients with KP infections was 28.69% (95% CI, 26.53%-30.86%). South Asia had the highest CRKP prevalence at 66.04% (95% CI, 54.22%-77.85%), while high-income North America had the lowest prevalence at 14.29% (95% CI, 6.50%-22.0%). In the country/territory level, Greece had the highest prevalence at 70.61% (95% CI, 56.77%-84.45%), followed by India at 67.62% (95% CI, 53.74%-81.79%) and Taiwan at 67.54% (95% CI, 58.65%-76.14%). Hospital-acquired CRKP infections were associated with the following factors: hematologic malignancies, corticosteroid therapies, intensive care unit stays, mechanical ventilations, central venous catheter implantations, previous hospitalization, and antibiotic-related exposures (antifungals, carbapenems, quinolones, and cephalosporins).

Conclusions

Study findings highlight the importance of routine surveillance to control carbapenem resistance and suggest that patients with nosocomial KP infection have a very high prevalence of CRKP.

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.

Phenotypic and genotypic detection of resistance mechanisms in carbapenem-resistant gram-negative bacteria isolated from Egyptian ICU patients with first emergence of NDM-1 producing Klebsiella oxytoca

Background and Objectives

Carbapenems are considered the last resort to treat several infections, particularly in intensive care units (ICUs). However, increasing carbapenem resistance is problematic because it leads to high morbidity and mortality rates. This study aimed to determine the rate of carbapenem resistance among Gram-negative bacteria collected from patients in ICUs and to identify their resistance mechanisms using phenotypic and genotypic methods.

Materials and Methods

Antimicrobial susceptibility testing was carried out using the disc diffusion method among 180 Gram-negative bacterial isolates. Productions of carbapenemases, metallo-beta-lactamases (MBLs) and the harboring of carbapenemase-encoding genes, were detected in 40 selected carbapenem-resistant Gram-negative bacteria (CR-GNB).

Results

Of 40 selected CR-GNB isolates, 28 (70%), and 20 (50%) isolates were phenotypically positive for carbapenemase, and MBL production, respectively. Furthermore, 22 (55%) showed amplification of one or more of the carbapenemase-encoding genes, including bla _NDM-1, bla _VIM-2, and bla _OXA-48. This study described the first emergence of NDM-1 producing Klebsiella oxytoca in Egyptian ICUs.

Conclusion

High incidence of CR-GNB detected in the ICUs in our study area may be attributed to the overuse of antibiotics, including carbapenems, and improper application of infection control measures. These findings confirm the need for the application of a strict antibiotic stewardship program.

Phenotypic and molecular characterization of extended-spectrum β-lactamase/AmpC- and carbapenemase-producing Klebsiella pneumoniae in Iran

BACKGROUND

The objective of the current study is to evaluate the phenotypic and molecular characterization of ESBL/AmpC- and carbapenemase-producing K. pneumoniae isolates in Iran.

METHODS

From October 2018 until the end of April 2020, different clinical samples were collected and K. pneumoniae isolates were identified using conventional biochemical tests and PCR assay. Antibiotic susceptibility pattern was determined using the Kirby-Bauer disk diffusion method. Modified Hedge Test (MHT) was applied to the identification of carbapenemase-producing K. pneumoniae. ESBL and AmpC-producing K. pneumoniae were detected using Double Disc Test (DDT) and Disc Potentiation Test (DPT), respectively. The presence of carbapenemase, ESBL, and AmpC encoding genes was screened by Polymerase Chain Reaction (PCR) assay.

RESULTS

A total of 100 K. pneumoniae isolates were collected. K. pneumoniae isolates had the highest resistance rate to cefazolin (66%) and cefotaxime (66%). Meropenem and amikacin with sensitivity rates of 76% and 69% were the most effective antimicrobial agents on K. pneumoniae isolates. It was found that 12 (12%), 27 (27%), and 9 (9%) K. pneumoniae isolates were positive in MHT, DDT, and DPT tests, respectively. Among the carbapenemase-encoding genes, bla_OXA-48 (24%) and bla_IMP (13%) genes had the highest frequency, while bla_KPC and bla_GIM genes were not detected among K. pneumoniae isolates. bla_TEM (48%) and bla_CMY (8%) genes had the highest frequency among ESBL and AmpC β-lactamase-encoding genes, respectively.

CONCLUSIONS

It is vital to adopt effective control strategies for K. pneumoniae infections and ensure rapid identification of antibiotic resistance profile.

A Rapid Antimicrobial Susceptibility Test for Klebsiella pneumoniae Using a Broth Micro-Dilution Combined with MALDI TOF MS

Background

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a novel method that can be used to identify pathogens and has potential applications in the detection of drug-resistant bacteria.

Purpose

To evaluate the ability of a MALDI-TOF MS-based broth micro-dilution method in detecting the minimum inhibitory concentration (MIC) values of Klebsiella pneumoniae to ceftriaxone and imipenem.

Materials and Methods

Sixty strains of K. pneumoniae with different levels of resistance to carbapenems and cephalosporins were randomly collected. The 0.5 McFarland (Mc) concentration of the bacterial suspension was inoculated in cation-adjusted Mueller-Hinton broth (CAMHB) with a final cell turbidity of 5×10⁵ CFU/mL. The broth was incubated with serial concentrations of antibiotics. After centrifuging the bacterial suspensions, the lysed cells were analyzed by MALDI-TOF MS to identify the growth-promoting or inhibitory effects on K. pneumoniae. The molecular mechanisms of resistance were investigated by PCR and DNA sequencing analysis.

Results

The expression of known resistance genes (blaKPC, blaFOX, blaDHA, blaCTX-M and blaTEM) was detected in the 30 carbapenems-resistant strains. The agreement between the MIC values derived from the MALDI-TOF MS analysis and from the broth micro-dilution method was 61.7% for ceftriaxone and 71.7% for imipenem. According to the Clinical and Laboratory Standards Institute (CLSI) breakpoint of resistance to ceftriaxone and imipenem, the 60 isolates were accurately classified as resistant or susceptible isolates with 100% sensitivity and 100% specificity.

Conclusion

The transmission and infection of multidrug-resistant bacteria could be better managed and treated with the rapid identification of strains and antimicrobial susceptibility. A MALDI-TOF MS-based susceptibility test could be used to identify resistance of K. pneumoniae within a short time-frame. This approach could potentially be used as a supplementary antimicrobial susceptibility test that could be investigated on more bacterial species combined with different antibiotics.

Prevalence and molecular epidemiology of carbapenem-resistant Gram-negative bacilli and their resistance determinants in the Eastern Mediterranean Region over the last decade

Carbapenem resistance in Enterobacteriaceae, Acinetobacter baumannii and Pseudomonas aeruginosa is increasing worldwide, which has led the World Health Organization (WHO) to list these bacteria in the critical priority pathogens group. Infections by such pathogens pose a serious threat to hospitalised patients and are associated with clinical and economic consequences. What worsens the case is the weak pipeline of available antimicrobial agents to treat such infections and the absence of new drugs. The aim of this review was to shed light on all studies tackling carbapenem resistance in Enterobacteriaceae, A. baumannii and P. aeruginosa in the Eastern Mediterranean region, with indication for each country, description of studies timeline, prevalence of carbapenem resistance, and carbapenem resistance-encoding genes detected in these countries.

Carbapenem-resistant Enterobacteriaceae (CRE) and gram-negative bacterial infections in south-west Nigeria: a retrospective epidemiological surveillance study

Background

Carbapenem-resistant Enterobacteriaceae (CRE) are often responsible for severe, life-threatening infections and they represent a critical threat to the available antibiotic agents and to global health. An understanding of the epidemiology of these infections will be indispensable to the development of appropriate case management as well as infection prevention and control (IPC) measures in any healthcare setting.

Objectives

The objective of this study was to investigate and describe the epidemiology of carbapenem-resistant Enterobacteriaceae (CRE) and other gram-negative bacteria in a tertiary hospital in south west Nigeria using routinely collected microbiological laboratory data.

Methods

A retrospective collection of microbiological laboratory records from the January to June 2018 was performed. All culture and antimicrobial susceptibility test results of patients who required laboratory tests were collected. Other information collected include: patient demographics, clinical specimen types and the requesting hospital department. The data was analyzed using SPSS Windows version 24. Comparison between categorical variables was done using chi-square tests while independent sample t-test was used to determine significant mean differences between groups. A p < 0.05 was taken to be statistically significant.

Results

The prevalence of carbapenem-resistance among Enterobacteriaceae and gram-negative bacteria isolates was 22% (n = 39/177). Of these, 35.9% (n = 14) were Klebsiella pneumonia, 30.8% (n = 12) were Pseudomonas aeruginosa and 15.4% (n = 6) were Klebsiella oxytoca. 87.2% (n = 34) of these were also multi-drug resistant, with a mean total resistance score of 3.92 (SD = ± 1.44). There were differences observed in proportion of carbapenem-resistance across clinical specialties and age groups; however, these differences were not statistically significant. Independent sample t-test revealed that carbapenem-resistant isolates exhibited more drug resistance than carbapenem-sensitive isolates (3.93 vs. 2.30; p < 0.001).

Conclusion

Carbapenem resistance is an important threat to the current antibiotic armory. Active surveillance, particularly in the healthcare setting is required to identify high risk groups, inform better treatment options and infection prevention and control measures.

Characterization of β-lactam resistance in K. pneumoniae associated with ready-to-eat processed meat in Egypt

K. pneumoniae was known as a nosocomial infection that causes human diseases. It is considered as one of the food-borne pathogens as it causes septicemia and diarrhea in humans. This study aims to characterize K. pneumoniae strains isolated from ready to eat processed meat phenotypically and genetically. Three hundred and fifty ready to eat processed meat (Luncheon-meat) samples were collected. Forty-four (12.6%) K. pneumoniae strains were isolated and bio-typed, where the majority were identified to belong to biotype B1. K1 and K2 serotypes were detected and strains were classified as hypermucoviscous K. pneumoniae (HVKP) and classic K. pneumoniae (CKP) (26 and 18 isolates, respectively). The isolates were resistant to several classes of β–lactam antibiotics, ceftazidim and cefotaxime (95.5%), cefoxitin (93.2%), ertapenem (90.9%) and amoxicillin-clavulanic acid (86.4%). They were classified as extended spectrum β–lactamases (ESBLs), AmpC or carbapenemase-producers phenotypically. Eighteen β-lactamase genes were investigated by PCR. The most prominent genes were SHV (63.6%), TEM (52.2%), CTX-M15 (50%), AMPC (47.7%), CIT-M (45.5%) and VIM (43.2%). Co-detection of β–lactam resistance genes revealed 42 gene profiles. Twenty-four isolates had the complete efflux system (AcrAB-ToƖC). Besides, Integrons (I, II, III) were detected in 20 isolates. Molecular typing by ERIC-PCR showed high genetic diversity between isolates as 34 different patterns were identified. Overall, this study confirmed the hazards posed by the presence of multiple resistance genes in the same isolate and this should not be undervalued. Besides, the horizontal transfer of plasmid harboring resistance genes between isolates in food represents potential health risks for consumers in Egypt and so the control and inhibition plans are necessary.