Detection and characterization of carbapenem resistant Gram-negative bacilli isolates recovered from hospitalized patients at Soba University Hospital, Sudan

Prevalence of genes encoding carbapenem-resistance in Klebsiella pneumoniae recovered from clinical samples in Africa: systematic review and meta-analysis

BACKGROUND

The potential of Klebsiella pneumoniae (K. pneumoniae) to acquire and spread carbapenem-resistant genes is the most concerning characteristic of the bacteria. In hospitals and other healthcare settings, multidrug-resistant K. pneumoniae can be prevalent and cause severe infections, posing significant challenges to patient management. Studying genetic variants and drug-resistant mutations in pathogenic bacteria of public health importance is essential. Therefore, this study aimed to assess the overall prevalence of carbapenemase-encoding genes in K. pneumoniae across Africa.

METHODS

All studies published between January 2010, and December 2023, were retrieved from the electronic databases PubMed, Science Direct, and Scopus, as well as through the Google Scholar search engine. This systematic review and meta-analysis adhered strictly to the PRISMA guidelines. Data analysis was performed using STATA version 17. The quality of the included studies was critically evaluated using the "Joanna Briggs Institute" criteria. To evaluate heterogeneity among the studies, inverse variance (I2) tests were utilized. Subgroup analysis was conducted when heterogeneity exists among studies. To assess publication bias, we used a funnel plot and Egger's regression test. A random effects model was used to calculate the weighted pooled prevalence of genetic variants associated with carbapenem resistance in K. pneumoniae.

RESULTS

A total of 49 potential studies were included in this systematic review and meta-analysis, encompassing 8,021 K. pneumoniae isolates. Among these isolates, 2,254 (28.1%) carbapenems-resistance-conferring genes were identified. The overall pooled prevalence of carbapenemase-encoding genes in K. pneumoniae isolated from clinical specimens across Africa was found to be 34.0% (95% CI: 26.01-41.98%). Furthermore, the pooled prevalence of the carbapenemase genes blaOXA-48 and blaNDM-1 was 16.96% (95% CI: 12.17-21.76%) and 15.08% (95% CI: 9.79-20.37%), respectively. The pooled prevalence of carbapenemase genes in K. pneumoniae isolates from clinical samples across Africa increased over time, reported as 20.4%(-0.7-41.4%) for 2010-2015, 34.5% (20.2-48.8%) for 2016-2020, and 35.2% (24.8-45.5%) for 2021-2023, with heterogeneity (I2) values of 36.5%, 96.7%, and 99.3%, respectively.

CONCLUSIONS

The emergence and spread of carbapenemase-encoding genes in K. pneumoniae pose a major threat to public health. Knowledge on the genetic mechanisms of carbapenem resistance is crucial for developing effective strategies to combat these multidrug-resistant infections and reduce their impact on healthcare systems. The carbapenemase genes blaOXA-48 and blaNDM-1 were the most prevalent and showed an increasing trend over time.

Molecular epidemiology of carbapenemase-producing Enterobacteriaceae and Acinetobacter baumannii in human infections around the Red Sea

The emergence and global spread of carbapenemase-producing bacteria (CPB) is of great concern to public health. Carbapenemase enzymes, which can hydrolyse almost all β-lactams, can be readily transferred between bacterial species through recombinant plasmids, transposons, or integrons. Human infections caused by CPB have limited treatment options and are associated with high mortality rates. These enzymes are mainly identified among Enterobacteriaceae and non-fermenter bacteria such as Acinetobacter baumannii and are associated either with hospital- or community-acquired infections. Located at the crossroads of the Middle East, Europe, and Africa, the countries around the Red Sea are of interest due to their great diversity and mix of populations. This review aims to describe the epidemiology of carbapenem resistance in Enterobacteriaceae and A. baumannii around the Red Sea, with country-specific findings. In this study, we emphasise the urgent need to screen for and detect these enzymes to prevent their spread and to maintain control.

Phenotypic identification of Metallo-ß- lactamase resistance Gram negative bacteria from a clinical specimen in Sidama, Ethiopia

BACKGROUND

Metallo-beta lactamase resistance is one of the carbapenem resistances that worsen the world nowadays. A new variant of carbapenem-resistant has only limited reports from Africa including Ethiopia. This study aimed to determine Metallo -ß- lactamase resistance Gram-negative bacteria in Hawassa University Comprehensive Specialized Hospital January-June 2023.

METHOD

A cross-sectional study was conducted in which consecutive patients infected with Gram-negative bacteria were included in the study. A structured questionnaire was used to collect the data with oriented nurses if the patients/or caregivers gave consent to participate in the study. Clinical specimens are processed based on the standard operating procedure of the Microbiology laboratory and Clinical laboratory standard institute guidelines. Culture and sensitivity testing was used to isolate the bacteria. Gram staining and biochemical tests was used to identify the bacteria to genus and species. Kirby disc diffusion technique was used to determine the susceptibility of antibiotics. Statistical Software for Social Science (SPSS) version 21 is used for data entry and analysis. Descriptive statistics and logistic regression were used to interpret the data. The odds ratio at 95% confidence interval (CI) and p-value < 0.05 were taken as a statistically significant association.

RESULT

Our study included 153 isolates from different specimens, 83 (54.2%) were from male patients and 70 (45.8%) were from females. Klebsiella pneumonia was the predominant 43, followed by Escherichia coli 32, Acinetobacter spp 25, Pseudomonas spp 15, Enterobacter agglomerus 9, Klebsiella ozaenae 6, Enterobacter cloacae 5, Klebsiella oxytoca 4, (Klebsiella rhinoscleromatis, Proteus mirabilis and Morganella morganii) 3, Providencia stuartii 2 and (Citrobacter spp & Proteus vulgaris) 1. The rates of multi, extensive and pan-drug resistance bacteria accounted for 128/153 (83.7%), 77 /153(50.3%), and 26/153 (17.0%), respectively. Carbapenem resistance was 21 (13.7%), of this 7.2% were Enterobacteriaceae, 5.2% were Acetinobacter spp. and 1.3% Pseudomonas spp. Metallo-beta-lactamase was 17 (11.1%), of this, Enterobacteriaceae were 9(5.9%), Acetinobacter spp. 7(4.6%), and Pseudomonas spp. 1(0.7%). There were no variables statistically significantly associated with metallo-beta-lactamase-resistant.

CONCLUSION

Our study revealed that Metallo-beta-lactamase resistance was circulating in the study area. There was a high rate of carbapenem resistance, multi, extensive and pan-drug resistance. Therefore, a measure should be taken to alleviate the emerging threat that leaves the patients without the option of treatment.

Rapid Detection of Carbapenemases Using NG-Test® CARBA 5 in Positive Blood Cultures: A Diagnostic Test Study

BACKGROUND

Infections due to carbapenem-resistant Gram-negative bacteria are emerging as an important challenge in health-care settings and a growing concern worldwide. Lateral flow immunoassay NG-Test® CARBA 5 can detect the five most reported carbapenemases (KPC, OXA-48-like, VIM, IMP, and NDM). Direct testing of positive blood cultures could reduce time to detection. This study aims to validate and report on the diagnostic yield of a novel method for carbapenemase detection in positive blood culture vials using NG-Test® CARBA 5.

METHODS

We implemented an investigator-developed method for the direct testing of positive blood cultures using NG-Test® CARBA 5. We compared results between genotypic, phenotypic, and direct NG-Test® CARBA 5 in blood.

RESULTS

A total of 32 isolates were tested (21 Enterobacterales and 11 Pseudomonas aeruginosa). Genotypic testing detected 23 carbapenemases. When comparing the results of NG-Test® CARBA 5 in blood with genotypic testing, agreement was observed in 31/32 (97%) tests. The sensitivity, specificity, positive predictive value, and negative predictive value of the NG-Test® CARBA 5 in blood were 93%, 100%, 100%, and 94%, respectively.

CONCLUSIONS

Our method using NG-Test® CARBA 5 directly in blood culture samples presented an excellent diagnostic yield when compared to genotypic profiling and permits an accurate detection of carbapenemases.

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.

Combatting resistance: Understanding multi-drug resistant pathogens in intensive care units

The escalating misuse and excessive utilization of antibiotics have led to the widespread dissemination of drug-resistant bacteria, posing a significant global healthcare crisis. Of particular concern is the increasing prevalence of multi-drug resistant (MDR) opportunistic pathogens in Intensive Care Units (ICUs), which presents a severe threat to public health and contributes to substantial morbidity and mortality. Among them, MDR ESKAPE pathogens account for the vast majority of these opportunistic pathogens. This comprehensive review provides a meticulous analysis of the current prevalence landscape of MDR opportunistic pathogens in ICUs, especially in ESKAPE pathogens, illuminating their resistance mechanisms against commonly employed first-line antibiotics, including polymyxins, carbapenems, and tigecycline. Furthermore, this review explores innovative strategies aimed at preventing and controlling the emergence and spread of resistance. By emphasizing the urgent need for robust measures to combat nosocomial infections caused by MDR opportunistic pathogens in ICUs, this study serves as an invaluable reference for future investigations in the field of antibiotic resistance.

Outbreak investigation of NDM-producing Burkholderia cepacia causing neonatal sepsis in Pakistan

Aim: To investigate the outbreak of Burkholderia cepacia complex (BCC), mortality, antimicrobial resistance and associated risk factors in the neonatal intensive care unit. Method: Eighteen blood culture samples from neonates and twenty swab samples from different neonatal intensive care unit surfaces were collected. The VITEK 2 was used to confirm the isolates and generate the antibiogram. PCR was used to identify blaNDM. Results: Eighteen samples tested positive for BCC, and 10/18 (55.5%) of the neonates died. 13/18 (72%) of the neonates had late-onset neonatal sepsis, and 10/18 (55%) had low birth weight. Resistance to minocycline and chloramphenicol was 100%, 72.2% to meropenem; 72.2% NDM gene was found in neonates and was 20% from the environment. Conclusion: Outbreak of NDM-producing BCC resulting in high neonatal mortality in NICU.

Comparative Investigation into the Roles of Imipenem:Cyclodextrin Complexation and Antibiotic Combination in Combatting Antimicrobial Resistance in Gram-Negative Bacteria

Extensively drug-resistant (XDR), multidrug-resistant (MDR) and pandrug-resistant (PDR) Gram-negative microorganisms (GNBs) are considered a significant global threat. β-lactam and aminoglycoside combinations and imipenem:cyclodextrin inclusion complexes were studied for the treatment of lethal GNBs. This is because of the broad empiric coverage of the two drugs and their possession of different spectra of activity. Two cyclodextrins (β- and hydroxy propyl β-cyclodextrins) were utilized for inclusion complex formation with imipenem using the physical and kneading methods. In silico investigation using the molecular docking and Fourier-infrared spectroscopy (FTIR) were employed to estimate binding constant and confirm complex formation, respectively. The in vitro effects of amikacin and imipenem combination in comparison to the effect of imipenem-β- and hydroxy propyl β-cyclodextrin (CD) complexes against Klebsiella spp. and Acinetobacter baumannii were studied. The isolated microorganisms' antimicrobial responsiveness to various antibiotics (19 antibiotics) was evaluated. It was found that piperacillin/tazobactam and gentamycin (resistance rates were 33.3% and 34%, respectively) were the most effective antimicrobials. The in vitro studies have been performed by the checkerboard technique and time-killing assay. The studied combination of amikacin and imipenem showed a substantial drop in bacterial count (p < 0.05). The in vitro studies demonstrated a synergism for the investigated combination. Conventional PCR was used in molecular studies to identify the resistance genes bla IMP and aac (6')-Ib. The blaIMP and aac (6')-Ib were recorded in 38.2% and 3.6% of the studied isolates, respectively. The in vitro studies showed synergistic effects among the tested antibiotics with FICIs of ≤0.5. Finally, the study compared the reduction in bacterial count between the tested antibiotic combinations and imipenem:CD physical and kneaded mixtures. Imipenem:CD inclusion complexes demonstrated a significant bacterial count reduction over the antibiotic combination. These results highlight the emerging role of CDs as safe biofunctional excipients in the combat against superbug bacterial resistance.

Carbapenem-Resistant Gram-Negative Bacilli Characterization in a Tertiary Care Center from El Bajio, Mexico

Carbapenem-resistant Gram-negative bacilli (CR-GNB) are a major public health concern. We aimed to evaluate the prevalence of CR-GNB and the frequency of carbapenemase-encoding genes in a tertiary referral center from El Bajio, Mexico. A cross-sectional study was conducted between January and October 2022; Gram-negative bacilli (GNB) were screened for in vitro resistance to at least one carbapenem. CR-GNB were further analyzed for carbapenemase-production through phenotypical methods and by real-time PCR for the following genes: blaKPC, blaGES, blaNDM, blaVIM, blaIMP, and blaOXA-48. In total, 37 out of 508 GNB were carbapenem-resistant (7.3%, 95% CI 5.2-9.9). Non-fermenters had higher rates of carbapenem resistance than Enterobacterales (32.5% vs. 2.6%; OR 18.3, 95% CI 8.5-39, p < 0.0001), and Enterobacter cloacae showed higher carbapenem resistance than other Enterobacterales (27% vs. 1.4%; OR 25.9, 95% CI 6.9-95, p < 0.0001). Only 15 (40.5%) CR-GNB had a carbapenemase-encoding gene; Enterobacterales were more likely to have a carbapenemase-encoding gene than non-fermenters (63.6% vs. 30.8%, p = 0.08); blaNDM-1 and blaNDM-5 were the main genes found in Enterobacterales; and blaIMP-75 was the most common for Pseudomonas aeruginosa. The mcr-2 gene was harbored in one polymyxin-resistant E. cloacae. In our setting, NDM was the most common carbapenemase; however, less than half of the CR-GNB showed a carbapenemase-encoding gene.

Phenotyping and Genotyping Evaluation of E. coli Produces Carbapenemase Isolated from Cancer Patients in Al-Basrah, Iraq

One of the most important nosocomial organisms that cause urinary tract infections (UTIs) in cancer patients is Escherichia coli. A significant cause of concern in managing UTIs is the development of carbapenem-resistant bacteria. Escherichia coli with carbapenem resistance has become a more serious problem, particularly in Iraq. In this regard, the present study aimed to estimate the prevalence of carbapenem-resistant E. coli in Al-Basrah, Iraq. Conventional tests and the Vitek®2 system were used to identify the isolates and determine the susceptibility of E.coli isolates to antimicrobials. In addition, E.coli isolates were tested by mCIM and eCIM methods. Moreover, the major carbapenemase genes, including blaSPM, blaIMP, blaVIM, and blaKPC were detected by polymerase chain reaction. In total, 120 urine samples were collected from cancer patients who were suspected of having urinary tract infections at Basrah Center of Oncology Al-Sader Teaching Hospital, Basrah, Iraq. Identification of bacterial growth by using biochemical tests revealed different bacterial species. The most frequent bacteria were E. coli (n=22, 53.65%) isolates. The results showed that 13 (59.09%) and 11 (50%) out of 22 E. coli isolates were positive for the production of carbapenemase, based on the eCIM and sCIM, respectively. The majority of E.coli in this study possessed the blaVIM gene (n=13, 59.1%), followed by the blaKPC gene (n=5, 22.73%), blaIMP gene (n=5, 22.73%), and blaSPM gene (n=4, 18.18%). There is a spread of more than one type of carbapenemase among the E. coli isolates collected from UTI cancer patients in Basrah Hospital. The E. coli identified in the current study had a strong capacity to produce carbapenemase enzymes against the four generations of antibiotics, including imipenem and meropenem antibiotics.

Resistance profiles and genotyping of extended-spectrum beta-lactamase (ESBL) -producing and non-ESBL-producing E. coli and Klebsiella from retail market fishes

Studies on antimicrobial resistance (AMR) profiles and epidemiological affirmation for AMR transmission are limited in fisheries and aquaculture settings. Since 2015, based on Global Action Plan on AMR by World Health Organization (WHO) and World Organization for Animal Health (OIE), several initiatives have been under taken to enhance the knowledge, skills and capacity to establish AMR trends through surveillance and strengthening of epidemiological evidence. The focus of this study was to determine the prevalence of antimicrobial resistance (AMR), its resistance profiles and molecular characterization with respect to phylogroups, antimicrobial resistance genes (ARGs), virulence genes (VGs), quaternary ammonium compounds resistance (QAC) genes and plasmid typing in retail market fishes. Pulse field gel electrophoresis (PFGE) to understand the genetic lineage of the two most important Enterobacteriaceae members, E. coli and Klebsiella sp. was performed. 94 fish samples were collected from three different sites viz., Silagrant (S1), Garchuk (S2) and North Guwahati Town Committee (NGTC) Region (S3) in Guwahati, Assam. Out of the 113 microbial isolates from the fish samples, 45 (39.82%) were E. coli; 23 (20.35%) belonged to Klebsiella genus. Among E. coli, 48.88% (n = 22) of the isolates were alerted by the BD Phoenix M50 instrument as ESBL, 15.55% (n = 7) as PCP and 35.55% (n = 16) as non-ESBL. E. coli (39.82%) was the most prevalent pathogen among the Enterobacteriaceae members screened and showed resistance to ampicillin (69%) followed by cefazoline (64%), cefotaxime (49%) and piperacillin (49%). In the present study, 66.66% of E. coli and 30.43% of Klebsiella sp. were categorized as multi drug resistance (MDR) bacteria. CTX-M-gp-1, with CTX-M-15 variant (47%), was the most widely circulating beta-lactamase gene, while other ESBL genes bla_TEM (7%), bla_SHV (2%) and bla_OXA-1-like (2%) were also identified in E. coli. Out of the 23 isolates of Klebsiella, 14(60.86%) were ampicillin (AM)-resistant (11(47.82%) K. oxytoca, 3(13.04%) K. aerogenes), whereas 8(34.78%) isolates of K. oxytoca showed intermediate resistance to AM. All Klebsiella isolates were susceptible to AN, SCP, MEM and TZP, although two K. aerogenes were resistant to imipenem. DHA and LAT genes were detected, respectively, in 7(16%) and 1(2%) of the E. coli strains while a single K. oxytoca (4.34%) isolate carried MOX, DHA and bla_CMY-2 genes. The fluoroquinolone resistance genes identified in E. coli included qnrB (71%), qnrS (84%), oqxB (73%) and aac(6)-Ib-cr (27%); however, in Klebsiella, these genes, respectively, had a prevalence of 87%, 26%, 74% and 9%. The E. coli isolates belonged to phylogroup A(47%), B1(33%) and D(14%). All of the 22(100%) ESBL E. coli had chromosome-mediated disinfectant resistance genes viz., ydgE, ydgF, sugE(c), mdfA while 82% of ESBL E. coli had emrE. Among the non-ESBL E. coli isolates, 87% of them showed the presence of ydgE, ydgF and sugE(c) genes, while 78% of the isolates had mdfA and 39% had emrE genes respectively. 59% of the ESBL and 26% of the non-ESBL E. coli had showed the presence of qacEΔ1. The sugE(p) was present in 27% of the ESBL-producing E. coli and in 9% of non-ESBL isolates. Out of the 3 ESBL-producing Klebsiella isolates, 2(66.66%) K. oxytoca isolates were found harboring plasmid-mediated qacEΔ1 gene while one (33.33%) K. oxytoca isolate had sugE(p) gene. IncFI was the most prevalent plasmid type detected in the isolates studied, with A/C (18%), P (14%), X, Y (9% each) and I1-Iγ (14%, 4%). 50% (n = 11) of the ESBL and 17% (n = 4) of the non-ESBL E. coli isolates harboured IncFIB and 45% (n = 10) ESBL and one (4.34%) non-ESBL E. coli isolates harboured IncFIA. Dominance of E. coli over other Enterobacterales and diverse phylogenetic profiles of E. coli and Klebsiella sp. suggests the possibility of contamination and this may be due to compromised hygienic practices along the supply chain and contamination of aquatic ecosystem. Continuous surveillance in domestic markets must be a priority in addressing antimicrobial resistance in fishery settings and to identify any unwarranted epidemic clones of E. coli and Klebsiella that can challenge public health sector.

Bacterial Resistance in Hospital-Acquired Infections Acquired in the Intensive Care Unit: A Systematic Review

PURPOSE

In this review we present the status of the prevalence of bacteria resistant to antibiotics and the main antibiotic resistance genes that are reported in infections acquired in intensive care units (ICU) around the world.

METHODS

A systematic review based on the PRISMA guide was carried out, from the Science Direct, Redalyc, Scopus, Hinari, Scielo, Dialnet, PLOS, ProQuest, Taylor, Lilacs and PubMed/Medline databases. Inclusion criteria of this review were original research study published in a scientific journal in a 10-year time span from 1 January 2017 and 30 April 2022.

RESULTS

A total of 1686 studies were identified, but only 114 studies were considered eligible for inclusion. Klebsiella pneumoniae and Escherichia coli resistant to carbapenems and producers of extended-spectrum β-lactamases (ESBL) are the most frequently isolated pathogens in ICUs in Asia, Africa and Latin America. The blaOXA and blaCTX were antibiotic resistance genes (ARG) most commonly reported in different geographic regions (in 30 and 28 studies, respectively). Moreover, multidrug-resistant (MDR) strains were reported in higher frequency in hospital-acquired infections. Reports of MDR strains vary between continents, with the majority of publications being in Asia and between countries, with Egypt and Iran being highlighted. There is a predominance of few bacterial clones with MDR phenotype, for example, clonal complex 5 Methicillin-Resistant Staphylococcus aureus (CC5-MRSA) circulates frequently in hospitals in the United States, clone ST23-K. pneumoniae is reported in India and Iran, and clone ST260 carbapenemase-producing P. aeruginosa in the United States and Estonia.

CONCLUSION

Our systematic review reveals that ESBL- and carbapenemase-producing K. pneumoniae and E. coli are the most problematic bacteria that are reported, mainly in tertiary hospitals in Asia, Africa, and Latin America. We have also found propagation of dominant clones with a high degree of MDR, becoming a problem due to its high capacity to cause morbidity, mortality and additional hospital costs.

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.

Activity of ceftolozane/tazobactam against clinical isolates of Pseudomonas aeruginosa from patients in the Middle East and Africa - Study for Monitoring Antimicrobial Resistance Trends (SMART) 2017-2020

OBJECTIVES

We evaluated the activity of ceftolozane/tazobactam (C/T), and comparators against clinical Pseudomonas aeruginosa isolates collected for the global Study for Monitoring Antimicrobial Resistance Trends (SMART) surveillance program in ten countries in the Middle East and Africa to augment scarce standardized surveillance data in this region.

METHODS

Minimum inhibitory concentrations (MICs) were determined using Clinical and Laboratory Standards Institute broth microdilution and interpreted with European Committee on Antimicrobial Susceptibility Testing breakpoints. P. aeruginosa isolates testing with C/T MIC >4 mg/l or imipenem MIC >2 mg/l were screened for β-lactamase genes.

RESULTS

C/T was active against 91.4% and 87.0% of P. aeruginosa isolates from the Middle East and Africa, respectively (14-21 and 7-16 percentage points higher than most β-lactam comparators, respectively). Considerable variation in susceptibility was seen across countries, which largely correlated with the observed prevalence of carbapenemases and/or extended-spectrum β-lactamases. Differences across countries were smaller for C/T than for the β-lactam comparators, ranging from 81% C/T-susceptible among isolates from Jordan to 95% for Qatar. Among subsets resistant to meropenem, ceftazidime, or piperacillin/tazobactam, C/T maintained activity against 51-73% of isolates from the Middle East and against 27-54% from Africa (where metallo-β-lactamase and GES carbapenemase rates were higher).

CONCLUSION

Given the desirability of β-lactam use among clinicians, C/T represents an important option in the treatment of infections caused by P. aeruginosa.

In Vitro and In Vivo Effect of Amikacin and Imipenem Combinations against Multidrug-Resistant E. coli

Introduction: The emergence of multidrug-resistant (MDR) E. coli has developed worldwide; therefore, the use of antibiotic combinations may be an effective strategy to target resistant bacteria and fight life-threatening infections. The current study was performed to evaluate the in vitro and in vivo efficacy of amikacin and imipenem alone and in combination against multidrug-resistant E. coli. Methods: The combination treatment was assessed in vitro using a checkerboard technique and time-killing curve and in vivo using a peritonitis mouse model. In resistant isolates, conventional PCR and quantitative real-time PCR techniques were used to detect the resistant genes of Metallo-β-lactamase gene Imipenemase (bla-_IMP) and aminoglycoside 6′-N-acetyltransferase (aac (6′)-Ib). Scanning electron microscopy was used to detect the morphological changes in the resistant isolates after treatment with each drug alone and in combination. In vitro and in vivo studies showed a synergistic effect using the tested antibiotic combinations, showing fractional inhibitory concentration indices (FICIs) of ≤0.5. Regarding the in vivo study, combination therapy indicated a bactericidal effect after 24 h. E. coli isolates harboring the resistant genes Metallo-β-lactamase gene Imipenemase (bla-_IMP) and aminoglycoside 6′-N-acetyltransferase (aac (6′)-Ib) represented 80% and 66.7%, respectively, which were mainly isolated from wound infections. The lowest effect on Metallo-β-lactamase gene Imipenemase (bla-_IMP) and aminoglycoside 6′-N-acetyltransferase (aac (6′)-Ib) gene expression was shown in the presence of 0.25 × MIC of imipenem and 0.5 × MIC of amikacin. The scanning electron microscopy showed cell shrinkage and disruption in the outer membrane of E. coli in the presence of the antibiotic combination. Amikacin and imipenem combination can be expected to be effective in the treatment and control of serious infections caused by multidrug-resistant (MDR) E. coli and the reduction in bacterial resistance emergence.

Detection of NDM Variants (bla NDM-1, bla NDM-2, bla NDM-3) from Carbapenem-Resistant Escherichia coli and Klebsiella pneumoniae: First Report from Nepal

Background

Increasing burden of carbapenem resistance among Enterobacterales is attributable to their ability to produce carbapenemase enzymes like metallo-beta-lactamase (MBL), Klebsiella pneumoniae carbapenemase (KPC), and OXA-type. This study aimed to determine the prevalence of carbapenemases and MBL genes ((bla_NDM-1,bla_NDM-1 and bla_NDM-3) among E. coli and K. pneumoniae isolates.

Methods

A total of 2474 urine samples collected during the study period (July–December 2017) were processed at the microbiology laboratory of Kathmandu Model Hospital, Kathmandu. Isolates of E. coli and K. pneumoniae were processed for antimicrobial susceptibility testing (AST) by disc diffusion method. Carbapenem-resistant isolates were subjected to Modified Hodge Test (MHT) for phenotypic confirmation, and inhibitor-based combined disc tests for the differentiation of carbapenemase (MBL and KPC). MBL-producing isolates were screened for NDM genes by polymerase chain reaction (PCR).

Results

Of the total urine samples processed, 19.5% (483/2474) showed the bacterial growth. E. coli (72.6%; 351/483) was the predominant isolate followed by K. pneumoniae (12.6%; 61/483). In AST, 4.4% (18/412) isolates of E. coli (15/351) and K. pneumonia (3/61) showed resistance towards carbapenems, while 1.7% (7/412) of the isolates was confirmed as carbapenem-resistant in MHT. In this study, all (3/3) the isolates of K. pneumoniae were KPC-producers, whereas 66.7% (10/15), 20% (3/15) and 13.3% (2/15) of the E. coli isolates were MBL, KPC and MBL/KPC (both)-producers, respectively. In PCR assay, 80% (8/10), 90% (9/10) and 100% (10/10) of the isolates were positive for bla_NDM-1, bla_NDM-2 and bla_NDM-3, respectively.

Conclusion

Presence of NDM genes among carbapenemase-producing isolates is indicative of potential spread of drug-resistant variants. This study recommends the implementation of molecular diagnostic facilities in clinical settings for proper infection control, which can optimize the treatment therapies, and curb the emergence and spread of drug-resistant pathogens.

Co-Occurrence of β-Lactam and Aminoglycoside Resistance Determinants among Clinical and Environmental Isolates of Klebsiella pneumoniae and Escherichia coli: A Genomic Approach

The presence of antimicrobial-resistance genes (ARGs) in mobile genetic elements (MGEs) facilitates the rapid development and dissemination of multidrug-resistant bacteria, which represents a serious problem for human health. This is a One Health study which aims to investigate the co-occurrence of antimicrobial resistance determinants among clinical and environmental isolates of K. pneumoniae and E. coli. Various bioinformatics tools were used to elucidate the bacterial strains' ID, resistome, virulome, MGEs, and phylogeny for 42 isolates obtained from hospitalized patients (n = 20) and environmental sites (including fresh vegetables, fruits, and drinking water) (n = 22). The multilocus sequence typing (MLST) showed that K. pneumoniae belonged to ten sequence types (STs) while the E. coli belonged to seventeen STs. Multidrug-resistant isolates harbored β-lactam, aminoglycoside resistance determinants, and MGE were detected circulating in the environment (drinking water, fresh vegetables, and fruits) and in patients hospitalized with postoperative infections, neonatal sepsis, and urinary tract infection. Four K. pneumoniae environmental isolates (7E, 16EE, 1KE, and 19KE) were multidrug-resistant and were positive for different beta-lactam and aminoglycoside resistance determinants. blaCTX-M-15 in brackets of ISEc 9 and Tn 3 transposases was detected in isolates circulating in the pediatrics unit of Soba hospital and the environment. This study documented the presence of bacterial isolates harboring a similar pattern of antimicrobial resistance determinants circulating in hospitals and environments. A rapid response is needed from stakeholders to initiate a program for infection prevention and control measures to detect such clones disseminated in the communities and hospitals.

Genome-wide identification of carbapenem-resistant Gram-negative bacterial (CR-GNB) isolates retrieved from hospitalized patients in Bihar, India

Carbapenemase-producing clinical isolates are becoming more common over the world, posing a severe public health danger, particularly in developing nations like India. Carbapenem-resistant Gram-negative bacterial (CR-GNB) infection has become a fast-expanding global threat with limited antibiotic choice and significant mortality. This study aimed to highlight the carbapenem-resistance among clinical isolates of hospital admitted patients in Bihar, India. A cross-sectional study was conducted with 101 clinical isolates of Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa. All GNB isolates were tested for their antimicrobial susceptibility using Kirby-Bauer disc diffusion method. Double disc synergy test / modified Hodge test (DDST/MHT) were used to detect carbapenemase production by these isolates. Subsequently, these isolates were evaluated for carbapenem-resistance genes using whole-genome sequencing method. The overall percentage of carbapenem-resistance among GNB was (17/101) 16.8%. The genomic analysis of antimicrobial-resistance (AMR) demonstrates a significantly high prevalence of blaCTX-M followed by blaSHV, blaTEM, blaOXA, and blaNDM β-lactam or carbapenem resistance genes among clinical isolates of GNB. Co-occurrence of blaNDM with other beta-lactamase-encoding genes was found in 70.6% of carbapenemase-producing isolates. Our study highlights the mechanism of carbapenem-resistance to curb the overwhelming threat posed by the emergence of drug-resistance in India.

Phenotype and genetic determination of resistance to common disinfectants among biofilm-producing and non-producing Pseudomonas aeruginosa strains from clinical specimens in Iran

BACKGROUND

Pseudomonas aeruginosa is a common pathogen in Hospitalized patients, and its various resistance mechanisms contribute to patient morbidity and mortality. The main aims of the present study were to assess the susceptibility of biofilm-producing and non-producing P. aeruginosa isolates to the five commonly used Hospital disinfectants, to evaluate the synergistic effect of selected disinfectants and Ethylene-diamine-tetra acetic acid (EDTA), and the effect of exposure to sub-inhibitory concentrations of Sodium hypochlorite on antimicrobial susceptibility test.

RESULTS

The results showed that sodium hypochlorite 5% and Ethanol 70% were the most and least effective disinfectants against P. aeruginosa, respectively. The addition of EDTA significantly increased the effectiveness of the selected disinfectants. The changes in the antibiotic-resistance profiles after exposure to sub-inhibitory concentrations of disinfectants were observed for different classes of antibiotics (Carbapenems, Aminoglycosides, Cephalosporins, Fluoroquinolones). As well as near the all isolates harbored efflux pump genes and 117 (97.5%) of isolates produced biofilm.

CONCLUSION

In the current study, the mixture of disinfectant and EDTA were the most suitable selection to disinfect Hospital surfaces and instruments. Also, it was clear that exposure to sub-inhibitory concentrations of Sodium hypochlorite results in resistance to some antibiotics in P. aeruginosa species. Strong and intermediate biofilm formers belonged to MDR/XDR strains. Future studies should include more complex microbial communities residing in the Hospitals, and more disinfectants use in Hospitals.

Detection of blaKPC and blaNDM carbapenemase genes among Klebsiella pneumoniae isolates in Addis Ababa, Ethiopia: Dominance of blaNDM

Background

Infections caused by Klebsiella pneumoniae have been difficult to control because of the worldwide emergence of carbapenem-resistant isolates mainly due to carbapenemase production. Information regarding carbapenemase-producing K. pneumoniae is still scarce in Ethiopia. Therefore, the current study aimed to determine the prevalence of carbapenemase-producing K. pneumoniae and to assess the occurrence of bla_NDM and bla_KPC carbapenemase genes_.

Methods

A cross-sectional study was conducted from September 2018 to February 2019 at Tikur Anbessa Specialized Hospital, Addis Ababa, Ethiopia. A total of 132 non-duplicate K. pneumoniae isolates were studied. Phenotypic confirmation of carbapenemase production was done by modified Carbapenem Inactivation Method (mCIM). Multiplex PCR was performed for the detection of carbapenemase-encoding genes bla_KPC, and bla_NDM.

Results

Out of the total 132 K. pneumoniae isolates, 39 (29.6%) were non-susceptible to one or more carbapenems. The prevalence of carbapenemase-producing isolates from the total was 28 (21.2%) with mCIM of which the most dominant gene was bla_NDM 26 (92.9%) and one isolate carried bla_KPC concomitantly. Carbapenemase-producing K. pneumoniae isolates were 100% non-susceptible to half of the antimicrobials used in the study, including meropenem and ertapenem. Previous use of carbapenems was associated with carbapenemase production (P = 0.004).

Conclusions

The prevalence of carbapenemase-producing K. pneumoniae isolates was worrying in the study area. To our knowledge, the study described the emergence of bla_NDM and bla_KPC gene carrying K. pneumoniae in Ethiopia for the first time. Further large-scale molecular-based studies, including other carbapenemase genes and sequencing of K. pneumoniae, are warranted to have a clear awareness about the presence of antimicrobial resistance high-risk clones in Ethiopia.

Establishment and validation of a nomogram to predict the in-hospital death risk of nosocomial infections in cancer patients

Background

Attributed to the immunosuppression caused by malignancy itself and its treatments, cancer patients are vulnerable to developing nosocomial infections. This study aimed to develop a nomogram to predict the in-hospital death risk of these patients.

Methods

This retrospective study was conducted at a medical center in Northwestern China. The univariate and multivariate logistic regression analyses were adopted to identify predictive factors for in-hospital mortality of nosocomial infections in cancer patients. A nomogram was developed to predict the in-hospital mortality of each patient, with receiver operating characteristic curves and calibration curves being generated to assess its predictive ability. Furthermore, decision curve analysis (DCA) was also performed to estimate the clinical utility of the nomogram.

Results

A total of 1,008 nosocomial infection episodes were recognized from 14,695 cancer patients. Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (15.5%) was the most predominant causative pathogen. Besides, multidrug-resistant strains were discovered in 25.5% of cases. The multivariate analysis indicated that Eastern Cooperative Oncology Group Performance Status 3–4, mechanical ventilation, septic shock, hypoproteinemia, and length of antimicrobial treatment < 7 days were correlated with higher in-hospital mortality. Patients who received curative surgery were correlated with favorable survival outcomes. Ultimately, a nomogram was constructed to predict the in-hospital mortality of nosocomial infections in cancer patients. The area under the curve values of the nomogram were 0.811 and 0.795 in the training and validation cohorts. The calibration curve showed high consistency between the actual and predicted in-hospital mortality. DCA indicated that the nomogram was of good clinical utility and more credible net clinical benefits in predicting in-hospital mortality.

Conclusions

Nosocomial infections stay conjoint in cancer patients, with gram-negative bacteria being the most frequent causative pathogens. We developed and verified a nomogram that could effectively predict the in-hospital death risk of nosocomial infections among these patients. Precise management of high-risk patients, early recognition of septic shock, rapid and adequate antimicrobial treatment, and dynamic monitoring of serum albumin levels may improve the prognosis of these individuals.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13756-022-01073-3.

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.

Virulence and Antibiotic Resistance Characteristics of Vibrio Isolates From Rustic Environmental Freshwaters

The study investigated the occurrence of antimicrobial resistance genes and virulence determinants in Vibrio species recovered from different freshwater sheds in rustic milieu. A total of 118 Vibrio isolates comprising Vibrio fluvialis (n=41), Vibrio mimicus (n=40) and V. vulnificus (n=37) was identified by amplification of ToxR, vmh and hsp60 genes. The amplification of virulence genes indicated that V. mimicus (toxR, zot, ctx, VPI, and ompU) genes were detected in 12.5%, 32.5%, 45%, 37.5% and 10% respectively. V. fluvialis genes (stn, hupO and vfh) were harboured in 48.8%, 14.6% and 19.5% isolates congruently. The other virulence genes that include vcgC and vcgE were observed in 63.1% and 29% of isolates belonging to V. vulnificus. With the exceptions of imipenem, meropenem and ciprofloxacin, most isolates exhibited more than 50% resistance to antibiotics. The antimicrobial resistance was more prevalent for polymyxin B (100%), azithromycin (100%) and least in ciprofloxacin (16.1%). Multiple antibiotic resistance index range was 0.3 and 0.8 with most isolates showing MARI of 0.8. The blaTEM, AmpC, blaGES, blaIMP, blaOXA-48 and blaKPC genes were detected in 53.3%, 42%, 29.6%, 16.6%, 15%, 11.3% and 5.6% of the isolates. Non-beta lactamases such as streptomycin resistance (aadA and strA), gentamicin resistance (aphA1) and quinolone resistance gene (qnrVC) were found in 5.2%, 44.3%, 26% and 2.8%. Chloramphenicol resistance genes (cmlA1 and catII) were found in 5.2% and 44.3% among the isolates. Our findings reveal the presence of antimicrobial resistance genes and virulent Vibrio species in aquatic environment which can have potential risk to human and animal's health.