High Carbapenem Resistance in Clinical Gram-Negative Pathogens Isolated in Egypt

Current Strategy for Targeting Metallo-β-Lactamase with Metal-Ion-Binding Inhibitors

Currently, antimicrobial resistance (AMR) is a serious health problem in the world, mainly because of the rapid spread of multidrug-resistant (MDR) bacteria. These include bacteria that produce β-lactamases, which confer resistance to β-lactams, the antibiotics with the most prescriptions in the world. Carbapenems are particularly noteworthy because they are considered the ultimate therapeutic option for MDR bacteria. However, this group of antibiotics can also be hydrolyzed by β-lactamases, including metallo-β-lactamases (MBLs), which have one or two zinc ions (Zn2+) on the active site and are resistant to common inhibitors of serine β-lactamases, such as clavulanic acid, sulbactam, tazobactam, and avibactam. Therefore, the design of inhibitors against MBLs has been directed toward various compounds, with groups such as nitrogen, thiols, and metal-binding carboxylates, or compounds such as bicyclic boronates that mimic hydrolysis intermediates. Other compounds, such as dipicolinic acid and aspergillomarasmin A, have also been shown to inhibit MBLs by chelating Zn2+. In fact, recent inhibitors are based on Zn2+ chelation, which is an important factor in the mechanism of action of most MBL inhibitors. Therefore, in this review, we analyzed the current strategies for the design and mechanism of action of metal-ion-binding inhibitors that combat MDR bacteria.

Molecular characterization of hypermucoviscous carbapenemase-encoding Klebsiella pneumoniae isolates from an Egyptian hospital

This study aimed to screen antibiotic resistance and virulence genes in carbapenem-resistant hypermucoviscous Klebsiella pneumoniae isolates from an Egyptian hospital. Among 38 previously confirmed carbapenem-nonsusceptible K. pneumoniae isolates, a string test identified three isolates as positive for hypermucoviscosity. Phenotypic characterization and molecular detection of carbapenemase- and virulence-encoding genes were performed. PCR-based multilocus sequence typing and phylogenetics were used to determine the clonality and global epidemiology of the strains. The coexistence of virulence and resistance genes in the isolates was analyzed statistically using a chi-square test. Three isolates showed the presence of carbapenemase-encoding genes (blaNDM, blaVIM, and blaIMP), adhesion genes (fim-H-1 and mrkD), and siderophore genes (entB); the isolates belonged to sequence types (STs) 101, 1310, and 1626. The relatedness between these sequence types and the sequence types of globally detected hypermucoviscous K. pneumoniae that also harbor carbapenemases was determined. Our analysis showed that the resistance and virulence profiles were not homogenous. Phylogenetically, different clones clustered together. There was no significant association between the presence of resistance and virulence genes in the isolates. There is a need for periodic surveillance of the healthcare settings in Egypt and globally to understand the true epidemiology of carbapenem-resistant, hypermucoviscous K. pneumoniae.

Biofilm formation and antimicrobial resistance pattern of uropathogenic E. coli ST131 isolated from children with malignant tumors

The multidrug-resistant clone identified as Escherichia coli sequence type 131 (E. coli ST131) has spread world-wide. This study sought to ascertain the frequency and biofilm formation of E. coli ST131 isolated from children with various malignancies. A total of 60 uropathogenic E. coli (UPEC) isolates from children without cancer and 30 UPEC isolates from children with cancer were assessed in this study. The microdilution method was used to investigate the sensitivity of bacteria to antibiotics. The microtiter plate (MTP) approach was used to phenotypically assess biofilm formation. The lasR, pelA, and lecA biofilm-encoding genes were detected by PCR in biofilm-producing isolates of E. coli. Thirty-seven out of 90 E. coli isolates were found to be ST131 (41.1%), with 17 (56.7%) from cancer-affected children and 20 (33.3%) from children without cancer, respectively (P-value = 0.036). The frequency of antimicrobial resistance was higher in ST131 strains were compared to non-ST131 strains and when they were isolated from healthy children vs. those who had cancer. In contrast to non-ST131 isolates, ST131 isolates were more biofilm-producers. There was a significant difference between the percentage of biofilm producers between the 22 (100%) ST131-O16 isolates and the 13 (86.7%) ST131-O25b isolates (P-value = 0.04). Children with cancer are more likely than children without cancer to develop biofilm forming E. coli ST131, the latter having a higher profile of antibiotic resistance. Interestingly, E. coli ST131 isolates from non-cancer patients had higher levels of overall antibiotic resistance and while more E. coli ST131isolates from cancer patients formed biofilms.

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.

Review and analysis of the overlapping threats of carbapenem and polymyxin resistant E. coli and Klebsiella in Africa

BACKGROUND

Carbapenem-resistant Enterobacterales are among the most serious antimicrobial resistance (AMR) threats. Emerging resistance to polymyxins raises the specter of untreatable infections. These resistant organisms have spread globally but, as indicated in WHO reports, the surveillance needed to identify and track them is insufficient, particularly in less resourced countries. This study employs comprehensive search strategies with data extraction, meta-analysis and mapping to help address gaps in the understanding of the risks of carbapenem and polymyxin resistance in the nations of Africa.

METHODS

Three comprehensive Boolean searches were constructed and utilized to query scientific and medical databases as well as grey literature sources through the end of 2019. Search results were screened to exclude irrelevant results and remaining studies were examined for relevant information regarding carbapenem and/or polymyxin(s) susceptibility and/or resistance amongst E. coli and Klebsiella isolates from humans. Such data and study characteristics were extracted and coded, and the resulting data was analyzed and geographically mapped.

RESULTS

Our analysis yielded 1341 reports documenting carbapenem resistance in 40 of 54 nations. Resistance among E. coli was estimated as high (> 5%) in 3, moderate (1-5%) in 8 and low (< 1%) in 14 nations with at least 100 representative isolates from 2010 to 2019, while present in 9 others with insufficient isolates to support estimates. Carbapenem resistance was generally higher among Klebsiella: high in 10 nations, moderate in 6, low in 6, and present in 11 with insufficient isolates for estimates. While much less information was available concerning polymyxins, we found 341 reports from 33 of 54 nations, documenting resistance in 23. Resistance among E. coli was high in 2 nations, moderate in 1 and low in 6, while present in 10 with insufficient isolates for estimates. Among Klebsiella, resistance was low in 8 nations and present in 8 with insufficient isolates for estimates. The most widespread associated genotypes were, for carbapenems, blaOXA-48, blaNDM-1 and blaOXA-181 and, for polymyxins, mcr-1, mgrB, and phoPQ/pmrAB. Overlapping carbapenem and polymyxin resistance was documented in 23 nations.

CONCLUSIONS

While numerous data gaps remain, these data show that significant carbapenem resistance is widespread in Africa and polymyxin resistance is also widely distributed, indicating the need to support robust AMR surveillance, antimicrobial stewardship and infection control in a manner that also addresses broader animal and environmental health dimensions.

Antibiotic resistance profile of common uropathogens during COVID-19 pandemic: hospital based epidemiologic study

BACKGROUND

Antimicrobial resistance has a direct impact on the ability to treat common infections, and this was worsened during the COVID-19 pandemic. Worldwide surveillance studies are lacking and resistance rates vary spatially, so frequent local surveillance reports are required to guide antimicrobial stewardship efforts. This study aims to report our common local uropathogens and their antibiogram profiles in our community during the COVID era.

METHODS

A retrospective study included patients referred to our urology units with urine culture and sensitivity. All bacterial strains were identified, and their antibiotic susceptibilities were tested.

RESULTS

Out of 2581 urine culture results recruited, 30% showed microbiological proof of infection. The majority, 486 (63.4%), were isolated from females. The most frequent isolates were Escherichia coli (44.4%) and Staphylococcus aureus (17.8%). The resistance rates ranged from 26.9 to 79.7%. Piperacillin-tazobactam antibiotic had the lowest resistance rate. The multi-drug resistance pattern was recorded in 181 (23.9%) of the isolates; 159/597 (26.6%) Gram-negative and 22/160 (13.8%) Gram-positive isolates.

CONCLUSIONS

Alarming rates of antimicrobial resistance were detected, which stresses the significance of following infection control policies and establishing national antimicrobial stewardship standards.

Magnitude and antimicrobial susceptibility profiles of Gram-Negative bacterial isolates among patients suspected of urinary tract infections in Arba Minch General Hospital, southern Ethiopia

The emergence of drug-resistant Gram-negative bacterial uropathogens poses a grave threat worldwide, howbeit studies on their magnitude are limited in most African countries, including Ethiopia. Therefore, measuring the extent of their drug resistance is essential for developing strategies to confine the spread. A cross-sectional study was conducted at title hospital from 01 June to 31 August 2020. Midstream urine specimens were collected and inoculated onto MacConkey agar. Positive urine cultures showing significant bacteriuria as per the Kass count (>105 CFU/mL) were further subjected to biochemical tests to identify the type of uropathogens. Antimicrobial susceptibility testing was performed by the Kirby-Bauer disk diffusion technique, and potential carbapenemase producers were phenotypically determined by the modified carbapenem inactivation method as per the CLSI guidelines. Data were analyzed using SPSS version 26; P-value <0.05 was considered statistically significant. Totally, 422 patients were included, and the majority were females (54.7%). The prevalence of carbapenem-resistant Gram-negative uropathogens was 12.9%, and 64.7% of them were carbapenemase producers. Klebsiella pneumoniae (n = 5) was the predominant carbapenemase producer, followed by Pseudomonas aeruginosa (n = 4). Consumption of antibiotics prior to six months of commencement of the study, the presence of chronic diseases and hospitalizations were statistically associated with UTI caused by carbapenem-resistant Gram-negative uropathogens. Carbapenemase producers were resistant to most of the antibiotics tested. Our findings highlight the need for periodic regional bacteriological surveillance programs to guide empirical antibiotic therapy of UTI.

Carbapenem-resistant Enterobacterales and Pseudomonas aeruginosa causing infection in Africa and the Middle East: a surveillance study from the ATLAS programme (2018–20)

Objectives

To determine the in vitro susceptibility of Enterobacterales (n = 5457) and Pseudomonas aeruginosa (n = 1949) isolated from hospitalized patients in Africa (three countries) and the Middle East (five countries) in 2018–20 to a panel of 11 antimicrobials and to identify β-lactamase/carbapenemase genes in isolates with meropenem-non-susceptible and/or ceftazidime/avibactam-resistant phenotypes.

Methods

CLSI broth microdilution testing generated MICs that were interpreted using CLSI (2021) breakpoints. β-Lactamase/carbapenemase genes were identified using multiplex PCR assays.

Results

Enterobacterales isolates were highly susceptible to amikacin (96.7%), ceftazidime/avibactam (96.6%) and tigecycline (96.0%), and slightly less susceptible to meropenem (94.3%). In total, 337 Enterobacterales isolates (6.2% of all Enterobacterales isolates) carried one or more carbapenemase genes: 188 isolates carried a serine carbapenemase (178 OXA, 10 KPC) and 167 isolates carried an MBL (18 isolates carried both an MBL and an OXA). NDM-1 was the most common MBL identified (64.1% of NDM enzymes; 59.9% of all MBLs). OXA-48 (47.8%) and OXA-181 (38.8%) were the most common OXAs detected. P. aeruginosa isolates were most susceptible to ceftazidime/avibactam (89.1%) and amikacin (88.9%). Only 73.1% of P. aeruginosa isolates were meropenem susceptible. The majority (68.1%) of P. aeruginosa isolates tested for carbapenemase/β-lactamase genes were negative. In total, 88 isolates (4.5% of all P. aeruginosa isolates) carried one or more carbapenemase genes: 81 isolates carried an MBL and 8 carried a GES carbapenemase (1 isolate carried genes for both).

Conclusions

Carbapenemase detection was closely associated with meropenem-non-susceptible phenotypes for Enterobacterales (89.1%) but not for P. aeruginosa (24.2%). Wide geographic variation in carbapenemase type and frequency of detection was observed.

Designing of a Novel Multi-Antigenic Epitope-Based Vaccine against E. hormaechei: An Intergraded Reverse Vaccinology and Immunoinformatics Approach

Enterobacter hormaechei is involved in multiple hospital-associated infections and is resistant to beta-lactam and tetracycline antibiotics. Due to emerging antibiotics resistance in E. hormaechei and lack of licensed vaccine availability, efforts are required to overcome the antibiotics crisis. In the current research study, a multi-epitope-based vaccine against E. hormaechei was designed using reverse vaccinology and immunoinformatic approaches. A total number of 50 strains were analyzed from which the core proteome was extracted. One extracellular (curlin minor subunit CsgB) and two periplasmic membrane proteins (flagellar basal-body rod protein (FlgF) and flagellar basal body P-ring protein (FlgI) were prioritized for B and T-cell epitope prediction. Only three filtered TPGKMDYTS, GADMTPGKM and RLSAESQAT epitopes were used when designing the vaccine construct. The epitopes were linked via GPGPG linkers and EAAAK linker-linked cholera toxin B-subunit adjuvant was used to enhance the immune stimulation efficacy of the vaccine. Docking studies of the vaccine construct with immune cell receptors revealed better interactions, vital for generating proper immune reactions. Docked complexes of vaccine with MHC-I, MHC-II and Tool-like receptor 4 (TLR-4) reported the lowest binding energy of −594.1 kcal/mol, −706.7 kcal/mol, −787.2 kcal/mol, respectively, and were further subjected to molecular dynamic simulations. Net binding free energy calculations also confirmed that the designed vaccine has a strong binding affinity for immune receptors and thus could be a good vaccine candidate for future experimental investigations.

Antimicrobial Susceptibility Testing of Clinical Isolates of Gram-Negative Bacilli Collected in Morocco by the ATLAS Global Surveillance Program from 2018 to 2020

OBJECTIVE

To report reference method antimicrobial susceptibility testing results for recent clinical isolates of Gram-negative bacilli from Morocco.

METHODS

CLSI broth microdilution antimicrobial susceptibility testing was performed by a central laboratory for isolates of Enterobacterales (n=810), Pseudomonas aeruginosa (n=321), and Acinetobacter baumannii (n=191) collected in 2018-2020 by three hospital laboratories in Morocco. MICs were interpreted using both CLSI (2021) and EUCAST (2021) breakpoints. Molecular testing for β-lactamase genes was performed on isolates meeting defined screening criteria.

RESULTS

Most isolates of Enterobacterales were susceptible (CLSI/EUCAST breakpoints) to amikacin (98.0%/96.2%), ceftazidime-avibactam (94.8%/94.8%), and meropenem (92.5%/94.2%). Of Enterobacterales isolates eligible for β-lactamase gene screening (n=210), 174 were ESBL-positive, 40 were metallo-β-lactamase-positive (all NDM), 39 were serine carbapenemase-positive (all OXA); and 7 isolates carried both OXA-48 and NDM-1. Amikacin (89.1%/89.1%) and ceftazidime-avibactam (88.2%/88.2%) were the most active agents tested against P. aeruginosa. Applying CLSI and EUCAST breakpoints, MDR rates were 21.9% and 29.3% for Enterobacterales and 18.4% and 21.8% for P. aeruginosa. Susceptible rates for amikacin, ceftazidime-avibactam, and meropenem were 93.2%/89.5%, 77.4%/82.3%, and 67.8%/80.2% for MDR Enterobacterales and 50.8%/57.1%, 40.7%/45.7%, and 27.1/32.9% for MDR P. aeruginosa. ≥70% of A. baumannii isolates were resistant to all agents tested (except colistin, EUCAST breakpoints only) including amikacin and meropenem.

CONCLUSION

Newer β-lactam/β-lactamase inhibitor combinations such as ceftazidime-avibactam warrant testing and reporting for Enterobacterales and P. aeruginosa in Morocco given the presence of significant resistance to first-line β-lactams and fluoroquinolones, pervasive ESBLs and carbapenemases, and toxicity concerns associated with some second-line agents.

Carriage of distinct blaKPC-2 and blaOXA-48 plasmids in a single ST11 hypervirulent Klebsiella pneumoniae isolate in Egypt

Background

Carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) causes serious infections with significant morbidity and mortality. However, the epidemiology and transmission mechanisms of CR-hvKP and the corresponding carbapenem-resistant plasmids require further investigation. Herein, we have characterized an ST11 K. pneumoniae strain EBSI041 from the blood sample encoding both hypervirulence and carbapenem resistance phenotypes from a patient in Egypt.

Results

K. pneumoniae strain EBSI041 showed multidrug-resistance phenotypes, where it was highly resistant to almost all tested antibiotics including carbapenems. And hypervirulence phenotypes of EBSI041 was confirmed by the model of Galleria mellonella infection. Whole-genome sequencing analysis showed that the hybrid plasmid pEBSI041-1 carried a set of virulence factors rmpA, rmpA2, iucABCD and iutA, and six resistance genes aph(3′)-VI, armA, msr(E), mph(E), qnrS, and sul2. Besides, bla_OXA-48 and bla_SHV-12 were harboured in a novel conjugative IncL-type plasmid pEBSI041-2. The bla_KPC-2-carrying plasmid pEBSI041-3, a non-conjugative plasmid lacking the conjugative transfer genes, could be transferred with the help of pEBSI041-2, and the two plasmids could fuse into a new plasmid during co-transfer. Moreover, the emergence of the p16HN-263_KPC-like plasmids is likely due to the integration of pEBSI041-3 and pEBSI041-4 via IS26-mediated rearrangement.

Conclusion

To the best of our knowledge, this is the first report on the complete genome sequence of KPC-2- and OXA-48-coproducing hypervirulent K. pneumoniae from Egypt. These results give new insights into the adaptation and evolution of K. pneumoniae during nosocomial infections.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08214-9.

High β-Lactam and Quinolone Resistance of Enterobacteriaceae from the Respiratory Tract of Sheep and Goat with Respiratory Disease

During the last decade's increase of antimicrobial resistance (AMR) in animals, animal-human transmission has become a major threat. Therefore, the present study aimed to evaluate the genetic basis of AMR in Gram-negative bacteria recovered from sheep and goats with respiratory disease. Nasal and ocular swabs were collected from 69 diseased animals, and 76 Gram-negative bacterial isolates were identified from 59 animals. All isolates were checked phenotypically for resistance and genotypically for different resistance mechanisms, including β-lactam, quinolone, and aminoglycoside resistance. Our results demonstrated that 9.2% (95% CI 4.5-17.8%) of the isolates were multidrug-resistant, with high resistance rates to β-lactams and quinolones, and 11.8% (95% CI 6.4-21%) and 6.6% (95% CI 2.8-14.5%) of the isolates were phenotypically positive for AmpC and ESBL, respectively. Genotypically, blaTEM was the most identified β-lactamase encoding gene in 29% (95% CI 20-40%) of the isolates, followed by blaSHV (14.5%, 95% CI 8.3-24.1%) and blaCTX-M (4%, 95% CI 1.4-11%). Furthermore, 7.9% (95% CI 3.7-16.2%) of the isolates harbored plasmid-mediated quinolone resistance gene qnrS. Our study revealed for the first time to our knowledge high β-lactam and quinolone resistance associated with the bacteria recovered from sheep and one goat with respiratory disease. Furthermore, different antimicrobial resistant determinants were identified for the first time from animals in Africa, such as blaLEN-13/55, blaTEM-176 and blaTEM-198/214. This study highlights the potential role of sheep and goats in disseminating AMR determinants and/or resistant bacteria to humans. The study regenerates interest for the development of a One Health approach to combat this formidable problem.

Co-Existence of Certain ESBLs, MBLs and Plasmid Mediated Quinolone Resistance Genes among MDR E. coli Isolated from Different Clinical Specimens in Egypt

The emergence of multi-drug resistant (MDR) strains and even pan drug resistant (PDR) strains is alarming. In this study, we studied the resistance pattern of E. coli pathogens recovered from patients with different infections in different hospitals in Minia, Egypt and the co-existence of different resistance determinants. E. coli was the most prevalent among patients suffering from urinary tract infections (62%), while they were the least isolated from eye infections (10%). High prevalence of MDR isolates was found (73%) associated with high ESBLs and MBLs production (89.4% and 64.8%, respectively). bla_TEM (80%) and bla_NDM (43%) were the most frequent ESBL and MBL, respectively. None of the isolates harbored bla_KPC and bla_OXA-48 carbapenemase like genes. Also, the fluoroquinolone modifying enzyme gene aac-(6′)-Ib-cr was detected in 25.2% of the isolates. More than one gene was found in 81% of the isolates. Azithromycin was one of the most effective antibiotics against MDR E. coli pathogens. The high MAR index of the isolates and the high prevalence of resistance genes, indicates an important public health concern and high-risk communities where antibiotics are abused.

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

Background

The noteworthy spread of carbapenem-resistant K. pneumoniae (CR-KP) isolates represents a significant safety threat.

Objective

Determination of the carbapenemase genes incidence among CR-KP clinical isolates in Kafrelsheikh, Egypt.

Methods

A total of 230 K. pneumoniae isolates were recovered from four hospitals in Kafrelsheikh, Egypt. Susceptibility testing was conducted using Kirby-Bauer method and automated-Vitek2 system. CR-KP isolates were tested using modified Hodge test (MHT) and combined disk synergy test. PCR and DNA sequencing were conducted for CR-KP isolates to recognize the included carbapenemase-genes.

Results

Out of 230 K. pneumoniae isolates, 50 isolates presented resistance to carbapenem (meropenem). All 50 CR-KP isolates were multidrug-resistant (MDR). Genes like blaNDM-1 and blaOXA-48 were the only detected genes among CR-KP with an incidence of 70.0% and 52.0%, respectively. Up to 74.0% of the tested isolates carried at least one of the two recorded genes, among them 48.0% co-harbored both blaNDM-1 and blaOXA-48 genes. The accession-numbers of sequenced blaNDM-1 and blaOXA-48 genes were MG594615 and MG594616, respectively.

Conclusion

This study reported a high incidence of MDR profile with the emergence of blaNDM-1 and blaOXA-48 genes co-existence in CR-KP isolates in Kafrelsheikh, Egypt. Hence, more restrictions should be applied against the spread of such serious pathogens.

Landscape of Multidrug-Resistant Gram-Negative Infections in Egypt: Survey and Literature Review

Purpose

This article is the first to review published reports on the prevalence of multidrug-resistant (MDR) gram-negative infections in Egypt and gain insights into antimicrobial resistance (AMR) surveillance and susceptibility testing capabilities of Egyptian medical centers.

Materials and Methods

A literature review and online survey were conducted.

Results

The online survey and literature review reported high prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (19–85.24% of E. coli, and 10–87% of K. pneumoniae), carbapenem-resistant Enterobacteriaceae (35–100% of K. pneumoniae and 13.8–100% of E. coli), carbapenem-resistant Acinetobacter baumannii (10–100%), and carbapenem-resistant Pseudomonas aeruginosa (15–70%) in Egypt. Risk factors for MDR Gram-negative infections were ventilated patients (67.4%), prolonged hospitalization (53.5%) and chronic disease (34.9%). Although antimicrobial surveillance capabilities were deemed at least moderate in most centers, lack of access to rapid AMR diagnostics, lack of use of local epidemiological data in treatment decision-making, lack of antimicrobial stewardship (AMS) programs, and lack of risk prediction tools were commonly reported by respondents.

Conclusion

This survey has highlighted the presence of knowledge gaps as well as limitations in the surveillance and monitoring capabilities of AMR in Egypt, with most laboratories lacking rapid diagnostics and molecular testing. Future efforts in Egypt should focus on tackling these issues via nationwide initiatives, including understanding the AMR trends in the country, capacity building of laboratories and their staff to correctly and timely identify AMR, and introducing newer antimicrobials for targeting emerging resistance mechanisms in Gram-negative species.

β-lactam resistance associated with β-lactamase production and porin alteration in clinical isolates of E. coli and K. pneumoniae

β-lactam resistance represents a worldwide problem and a serious challenge for antimicrobial treatment. Hence this research was conducted to recognize several mechanisms mediating β-lactam resistance in E. coli and K. pneumoniae clinical isolates collected from Mansoura University hospitals, Egypt. A total of 80 isolates, 45 E. coli and 35 K. pneumoniae isolates, were collected and their antibiotic susceptibility was determined by the Disc diffusion method followed by phenotypic and genotypic detection of extended-spectrum β-lactamases (ESBLs), AmpC β-lactamase, carbapenemase enzymes. The outer membrane protein porins of all isolates were analyzed and their genes were examined using gene amplification and sequencing. Also, the resistance to complement-mediated serum killing was estimated. A significant percentage of isolates (93.8%) were multidrug resistance and showed an elevated resistance to β-lactam antibiotics. The presence of either ESBL or AmpC enzymes was high among isolates (83.75%). Also, 60% of the isolated strains were carbapenemase producers. The most frequently detected gene of ESBL among all tested isolates was bla_CTX-M-15 (86.3%) followed by bla_TEM-1 (81.3%) and bla_SHV-1 (35%) while the Amp-C gene was present in 83.75%. For carbapenemase-producing isolates, bla_NDM1 was the most common (60%) followed by bla_VIM-1 (35%) and bla_OXA-48 (13.8%). Besides, 73.3% and 40% of E. coli and K. pneumoniae isolates respectively were serum resistant. Outer membrane protein analysis showed that 93.3% of E. coli and 95.7% of K. pneumoniae isolates lost their porins or showed modified porins. Furthermore, sequence analysis of tested porin genes in some isolates revealed the presence of frameshift mutations that produced truncated proteins of smaller size. β-lactam resistance in K. pneumoniae and E. coli isolates in our hospitals is due to a combination of β-lactamase activity and porin loss/alteration. Hence more restrictions should be applied on β-lactams usage to decrease the emergence of resistant strains.

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.

Detection of harmful foodborne pathogens in food samples at the points of sale by MALDT-TOF MS in Egypt

OBJECTIVES

Microbes can contaminate foodstuffs resulting in foodborne illnesses. Investigating microbial hazards in foods at the point of sale with rapid tools is required to avoid foodborne illness outbreaks. The current study aimed to identify the microbial hazards in food samples collected from retail shops at sale points using MALDI-TOF MS.

RESULTS

Food samples were collected from stores and supermarkets in four Delta cities (Tanta, Kutour, Kafr-Elzayat and Benha). Analysis of 178 samples of fish, meat and dairy products revealed 20 different bacterial species. 44.76% of isolates were identified as E. coli, 17.44% were identified as Enterobacter spp., and E. cloacae was predominant. 12.2% were identified as Citrobacter spp., and C. braakii was predominant, and 8.7% were identified as Klebsiella spp., and K. pneumoniae was predominant. Moreover, eight Proteus mirabilis, six Morganella morganii, five Staphylococcus hominis, three Serratia marcescens, two Pseudomonas aeruginosa, one Salmonella typhimurium and one Enterococcus faecalis were detected. Foodstuffs not only be contaminated during production and processing but also during storage and transport. Identification of harmful human pathogens in foodstuffs is alarming and consider threatening to public health. Identification of microbiological hazards in foods using MALDI-TOF MS provides an efficient tool for identifying foodborne pathogens.

The effect of EDTA in combination with some antibiotics against clinical isolates of gram negative bacteria in Mansoura, Egypt

Extensive use of antibiotics in clinical practice has been associated with increasing frequency of resistant microorganisms. So new strategy is needed to treat the resistant pathogens. Hence this study was conducted to determine the effect of Ethylenediaminetetraacetic acid (EDTA) in increasing the inhibition effect of some antibiotics on multi-drug resistant (MDR) gram-negative bacteria. For this purpose, 40 E. coli isolates, 40 K. pneumoniae isolates and 50 P. aeruginosa isolates were collected from different University's hospitals in Mansoura, Egypt. Antibacterial susceptibility pattern against 9 different antimicrobials were studied by disc diffusion method. Also the effect of two sub-inhibitory concentrations of EDTA (1 and 2 mM) on the inhibition zones of antibiotic discs against the highly multidrug resistant (MDR) isolates was determined. Checkerboard method was used for testing the activity of gentamicin/EDTA and cefotaxime/EDTA combinations on the highly MDR isolates. Additionally, the effect of EDTA on the expression of efflux pump genes was tested by real time-PCR. Most of the clinical isolates were found to be resistant to the tested antibiotics except imipenem and high prevalence of MDR isolates was recorded. 34 isolates were selected as those showed the highest multi-drug resistance and were tested to specify their MIC for EDTA as EDTA showed strong antibacterial activity with MIC ranging 4-8 mM. The addition of sub-MIC of EDTA (1or 2 mM) to the agar plate resulted in changing the 11 tested E. coli isolates from resistant to sensitive to ceftazidime, gentamicin, rifampin, ampicillin, erythromycin and vancomycin, the tested K. pneumoniae isolates were turned also from resistant to sensitive to gentamicin and ceftazidime, additionally the tested P. aeruginosa isolates became sensitive to gentamicin, ceftazidime and ciprofloxacin. Indifference to additive activity was observed for tested combinations and MIC value of cefotaxime or gentamicin in combination with EDTA was less than antibiotic alone in the most tested isolates. Moreover, significant reduction (P < 0.01) in the expression of all tested efflux pump genes in treated E. coli, K. pneumoniae and P. aeruginosa isolates with EDTA compared to untreated isolates was observed. In conclusion, these results suggest that the combination of antibiotic especially gentamicin with EDTA may be fruitful for management of resistant gram negative infections.

High β-lactam resistance in Gram-negative bacteria associated with kennel cough and cat flu in Egypt

Antimicrobial resistance within pets has gained worldwide attention due to pets close contact with humans. This report examined at the molecular level, the antimicrobial resistance mechanisms associated with kennel cough and cat flu. 1378 pets in total were assessed for signs of respiratory infection, and nasal and conjunctival swabs were collected across 76 diseased animals. Phenotypically, 27% of the isolates were characterized by multidrug resistance and possessed high levels of resistance rates to β-lactams. Phenotypic ESBLs/AmpCs production were identified within 40.5% and 24.3% of the isolates, respectively. Genotypically, ESBL- and AmpC-encoding genes were detected in 33.8% and 10.8% of the isolates, respectively, with bla_SHV comprising the most identified ESBL, and bla_CMY and bla_ACT present as the AmpC with the highest levels. qnr genes were identified in 64.9% of the isolates, with qnrS being the most prevalent (44.6%). Several antimicrobial resistance determinants were detected for the first time within pets from Africa, including bla_CTX-M-37, bla_CTX-M-156, bla_SHV-11, bla_ACT-23, bla_ACT25/31, bla_DHA-1, and bla_CMY-169. Our results revealed that pets displaying symptoms of respiratory illness are potential sources for pathogenic microbes possessing unique resistance mechanisms which could be disseminated to humans, thus leading to the development of severe untreatable infections in these hosts.

Molecular Characterization of Carbapenemase-Producing Klebsiella pneumoniae Isolated from Egyptian Pediatric Cancer Patients Including a Strain with a Rare Gene-Combination of β-Lactamases

PURPOSE

Healthcare-associated infections caused by multi-drug-resistant (MDR) pathogens are a global threat. We aim to assess the clonal relatedness among carbapenemase-producing Klebsiella pneumoniae (CPKP) strains infecting Egyptian pediatric cancer patients.

MATERIALS AND METHODS

Identification and antimicrobial susceptibility testing of 149 Gram-negative isolates obtained from pediatric cancer patients were performed by VITEK 2. Genes encoding carbapenemases and extended-spectrum β-lactamases were detected by PCR and verified by DNA sequencing of representative samples. The transferability of the plasmids harboring bla OXA-48, from representative clinical samples, was evaluated by performing a conjugation experiment followed by PCR and MIC shift determination. Clonal relationships among the bla OXA-48-harboring K. pneumoniae isolates were determined by enterobacterial repetitive intergenic consensus (ERIC)-PCR and pulsed-field gel electrophoresis (PFGE).

RESULTS

Carbapenem resistance was observed in 59% of the isolates. The most prevalent species was K. pneumoniae (45.6%) and 57% of them were isolated from ICU. Fifty-nine % of the K. pneumoniae isolates were carbapenemase-producers and bla OXA-48 was detected in (58%) of them. One isolate co-harbored bla OXA-48, bla NDM-1, and bla IMP-1 genes for the first time in Egypt. PCR and meropenem MIC shift confirmed the success of the transferability of representative plasmids to E. coli K12. ERIC and PFGE identified 93% and 100% of the K. pneumoniae with a similarity coefficient ≥85%, respectively, including strains with indistinguishable patterns, suggesting possible clonal dissemination.

CONCLUSION

Our findings underline the dissemination of diverse clones of MDR CPKP among Egyptian pediatric cancer patients. Hence, routine molecular characterizations followed by strict implementation of infection control measures are crucial to tackling this threat.

Global evolutionary epidemiology and resistome dynamics of Citrobacter species, Enterobacter hormaechei, Klebsiella variicola, and Proteeae clones

Citrobacter spp., Enterobacter hormaechei subsp., Klebsiella variicola and Proteae tribe members are rarely isolated Enterobacterales increasingly implicated in nosocomial infections. Herein, we show that these species contain multiple genes encoding resistance to important antibiotics and are widely and globally distributed, being isolated from human, animal, plant, and environmental sources in 67 countries. Certain clones and clades of these species were internationally disseminated, serving as reservoirs and mediums for the global dissemination of antibiotic resistance genes. As they can easily transmit these genes to more pathogenic species, additional molecular surveillance studies should be undertaken to identify and contain these antibiotic-resistant species.

Cross-border spread of bla NDM-1- and bla OXA-48-positive Klebsiella pneumoniae: a European collaborative analysis of whole genome sequencing and epidemiological data, 2014 to 2019

Analysis of sequencing data for 143 bla_NDM-1- and bla_OXA-48-positive Klebsiella pneumoniae isolates from 13 European national collections and the public domain resulted in the identification of 15 previously undetected multi-country transmission clusters. For 10 clusters, cases had prior travel/hospitalisation history in countries outside of the European Union including Egypt, Iran, Morocco, Russia, Serbia, Tunisia and Turkey. These findings highlight the benefit of European whole genome sequencing-based surveillance and data sharing for control of antimicrobial resistance.

Carbapenemase-Producing Non-Glucose-Fermenting Gram-Negative Bacilli in Africa, Pseudomonas aeruginosa and Acinetobacter baumannii: A Systematic Review and Meta-Analysis

Background

Studies have reported that the existence of CP bacteria in Africa, but, in general, comprehensive data about the molecular epidemiology of CP organisms are limited. Therefore, this systematic review and meta-analysis expound the pooled prevalence of CP P. aeruginosa and CP A. baumannii clinical isolates in Africa. It also identified the diversity of carbapenemases or their encoding genes among the isolates in Africa. Lastly, the review observed the trends of these CP isolates in Africa.

Methods

A comprehensive search was performed between July 2019 and October 2019 in the following databases: PubMed, Google Scholar, and African Journal online. The included articles were published only in English. The screening was done by two authors independently. The data extracted on Excel spreadsheet were transferred to STATA 11 software for analysis.

Results

From a total of 1,454 articles searched, 42 articles were eligible. Most of the studies were conducted in the North Africa region. But there was no report from Central Africa. The pooled prevalence of CP P. aeruginosa and CP A. baumannii among the clinical specimens in Africa was 21.36% and 56.97%, respectively. OXA-23 and VIM were the most prevailing carbapenemase among P. aeruginosa and A. baumannii, respectively. The cumulative meta-analysis revealed a relative increment of the prevalence of CP P. aeruginosa over time in Africa but it showed a higher prevalence of CP A. baumannii isolates across years.

Conclusion

The review revealed a high pooled prevalence of CP A. baumannii clinical isolates in Africa which needs urgent action. Moreover, the emergence of concomitant carbapenemases, especially OXA-23 +  NDM among CP A. baumannii, was also an alarming problem.

First Genomic Characterization of blaVIM-1 and mcr-9-Coharbouring Enterobacter hormaechei Isolated from Food of Animal Origin

We describe here the complete genome sequence of an Enterobacter hormaechei ST279 coharbouring bla_VIM-1 and mcr-9 recovered from uncooked beef patty in June 2017, Egypt. The tested isolate was resistant to carbapenem but susceptible to colistin (minimum inhibitory concentration (MIC), 0.5 μg/mL). The antimicrobial susceptibility profile and conjugation experiments were performed. The entire genome was sequenced by the Illumina MiniSeq and Oxford Nanopore methods. The bla_VIM-1 and mcr-9 genes are carried on the same IncHI2/pMLST1 plasmid, pMS37a (Size of 270.9 kb). The mcr-9 gene was located within the physical boundaries demarcated by two insertion elements IS903 (upstream) and IS1 (downstream) but did not possess the downstream regulatory genes (qseC/qseB) which regulate the expression of mcr-9. Therefore, the mcr-9 might be silently disseminated among carbapenem-resistant Enterobacterales. In addition to bla_VIM-1 and mcr-9, plasmid pMS37a harbored various antibiotic resistance genes including aac(6’)-Il, ΔaadA22, aac(6’)-Ib-cr, sul1, dfrA1 and tetA. To the best of our knowledge, this is the first report of a bla_VIM-1 and mcr-9-coharbouring E. hormaechei isolate of food origin worldwide. The identification of a multidrug-resistant VIM-1 and mcr-9 positive Enterobacter hormaechei isolate from food is worrisome as retail meat and meat products could serve as a vehicle for these MDR bacteria, which could be transferred between animals and humans through the food chain. It further highlights that Enterobacterales co-producing MCR and carbapenemases being found in the food chain indeed correspond to a One-Health issue, highlighting the need for serious steps to prevent their further dissemination.

Genetic Characterization of Carbapenemase-Producing Enterobacter cloacae Complex and Pseudomonas aeruginosa of Food of Animal Origin from Egypt

The increasing spread of carbapenem resistance is a serious global public health concern that negatively affects human and animal health. In this study we characterized the carbapenemase production in gram-negative bacteria isolated from different meat and meat products in Egypt. Phenotypic and genotypic susceptibility testing were investigated. Two Enterobacter cloacae complex strains, isolated from kofta and beef burger, and one Pseudomonas aeruginosa isolated from minced meat, were found to harbor VIM-1 and VIM-2, respectively. These isolates showed multidrug resistance phenotype. The phenotypic carbapenemase production was confirmed with Carba NP test in addition to modified Hodge test, modified carbapenem inactivation method, and ethylenediaminetetraacetic acid inhibition test. The bla_VIM-1 gene in both non-clonally related E. cloacae complex strains was part of a class 1 integron that also carried other resistance gene cassettes such as aacA7, dfrA1, ΔaadA, and smr. This integron was uncommonly disrupted by the insertion sequence ISPa21, located on a self-conjugative plasmid of either the A/C or HI2 incompatibility group with a size of >93 kb. The bla_VIM-2 gene was identified within a class 1 integron, followed downstream by resistance genes aadB and bla_OXA-10. The transfer of bla_VIM-2 gene from P. aeruginosa failed, suggesting that this gene was located on the chromosome. Further studies are needed to screen the dissemination of carbapenemase-producing bacteria in both the environment and food chain.

Comparative Evaluation of Five Assays for Detection of Carbapenemases with a Proposed Scheme for Their Precise Application

The escalating problem of the dissemination of carbapenemase-producing bacteria (CPB) has gained worldwide attention. The prompt diagnosis of CPB and precise identification of carbapenemases are imperative to enable specific antibiotic therapy and control the spread of these bacteria. The present study was designed to assess the performance of five important assays for the detection of carbapenemases. The modified carbapenem inactivation method (mCIM), CARBA-5, GeneXpert Carba-R, BD MAX Check-Points CPO, and GeneFields CPE assays were evaluated with an international collection of 159 bacterial isolates, including 93 CPB and 66 non-CPB isolates. The overall accuracy/sensitivity/specificity for carbapenemase detection were 100% (95% CI, 97.7%-100%)/100% (95% CI, 96.1%-100%)/100% (95% CI, 94.6%-100%) for mCIM, 98.7% (95% CI, 95.5%-99.9%)/97.9% (95% CI, 92.5%-99.7%)/100% (95% CI, 94.6%-100%) for CARBA-5, 96.9% (95% CI, 92.8%-99%)/95.7% (95% CI, 89.4%-98.8%)/98.5% (95% CI, 91.8%-99.9%) for GeneXpert Carba-R, 94.3% (95% CI, 89.5%-97.4%)/90.3% (95% CI, 82.4%-95.5%)/100% (95% CI, 94.6%-100%) for BD MAX Check-Points CPO, and 86.2% (95% CI, 79.8%-91.1%)/77.4% (95% CI, 67.6%-85.5%)/98.5% (95% CI, 91.8%-100%) for GeneFields CPE. Interestingly, mCIM and CARBA-5 assays showed 100% accuracy/sensitivity/specificity for detection of the target genes. Furthermore, all the other assays showed comparable high accuracy (96.9% to 100%), sensitivity (100%), and specificity (96.4% to 100%) for the detection of the target genes. On the basis of these results, a new scheme was proposed for their efficient application. These results confirmed the high sensitivity of the evaluated assays, and the proposed scheme is reliable and improves the overall sensitivity and specificity of the assays.

Ringing bells: Morganella morganii fights for recognition

OBJECTIVES

The global increase in rare opportunistic microbial infections is alarming. The current review was undertaken to study the diversified disease spectrum, pathogenicity, and resistance patterns of Morganella morganii.

STUDY DESIGN

This study is a review of the diversified disease spectrum of M. morganii.

METHODS

The articles used in this review were all extracted from PubMed and Google Scholar, using the terms 'M. morganii', 'prevalence', 'virulence factors', 'infections', 'resistance pattern', and 'genomics'. This review includes original articles, reviews, and case reports focusing on M. morganii, hospital-based prevalence studies, and studies on resistance in M. morganii published between 1906 and April 2019. Articles published in English, French, Spanish, and Chinese were reviewed.

RESULTS

M. morganii has had a significant impact as a clinical pathogen and the pace of its occurrence and the increase in its resistance rates puts this bacterium on the path to becoming the next 'superbug'. These developments not only impact M. morganii, but as a result of gene and plasmid transfer evolution, other clinical pathogens have been able to acquire their diverse intrinsic and acquired virulence genes. Its vast host range raises concerns around its capacity to generate new infections through novel symbiotic relationships.

CONCLUSIONS

M. morganii opportunism is being increasingly reported across the globe. This bacterium is accumulating intrinsic and acquired multidrug resistance genes, resulting in increased morbidity and mortality rates for M. morganii infections and complicating its treatment. M. morganii should be recognized as a clinically significant pathogen, and clinicians should place this microorganism in the list of causative possibilities during patient care. It is important for both the infection control activities in hospitals and in public health sector.

Molecular characterization of multidrug-resistant Gram-negative pathogens in three tertiary hospitals in Cairo, Egypt

High rates of antimicrobial resistance (AMR) among Gram-negative pathogens (GNP) have been reported in Egypt. Antimicrobial surveillance and identifying the genetic basis of AMR provide important information to optimize patient care. In this study, we aimed to identify the beta-lactam resistance phenotypes and genotypes of multidrug-resistant (MDR) non-repetitive GNP from 3 tertiary hospitals in Egypt. WZe studied 495 non-repetitive MDR Gram-negative isolates from patients with complicated intra-abdominal infections (cIAI), complicated urinary tract infection (cUTI), and lower respiratory tract infection (LRTI), collected as part of the “Study for Monitoring Antimicrobial Resistance Trends” (SMART) conducted in 3 tertiary hospitals in Cairo, Egypt, from 2015 to 2016. Identification and susceptibility testing of GNP to antimicrobials were tested in each hospital laboratory and confirmed in a reference laboratory (International Health Management Associates (IHMA), Inc., Schaumburg, IL, USA). Molecular identification of extended-spectrum beta-lactamases (ESΒLs), AmpC, and carbapenem resistance genes was conducted in IHMA. Among the 495 MDR isolates, Klebsiella pneumoniae (K. pneumoniae) and Escherichia coli (E. coli) were the most common (52.7% and 44.2%). K. pneumoniae was most susceptible to colistin, amikacin, ertapenem, and imipenem (92.7%, 72.7%, 69.3%, and 64%, respectively). E. coli was most susceptible to colistin (100%), amikacin (94.1%), imipenem (90.4%), and ertapenem (83.6%). ESBL was detected in 96.2% and ESBL genotypes included bla_CTX-M-15 (70.1%), bla_TEM-OSBL (48.5%), bla_SHV-OSBL (27.9%), and bla_CTX-M-14 (10.7%). AmpC resistance genes were identified in 9.7% of the isolates, dominated by bla_CMY-2 (5.7%). Carbapenem resistance genes were detected in 45.3% of the isolates. In K. pneumoniae, bla_OXA-48 dominated (40.6%), followed by bla_NDM-1 (23.7%) and bla_OXA-232 (4.5%). In E. coli, the most frequent genes were bla_NDM-5 (9.6%), bla_OXA-181 (5.5%), bla_OXA-244 (3.7%), and bla_NDM-1 (3.7%). bla_KPC-2 was identified in 0.4% of isolates. Notably, 32.3% of isolates carried more than one resistance gene. Our findings emphasize the continued need for molecular surveillance of MDR pathogens, implementation of strict infection control measures, and antimicrobial stewardship policies in our hospitals.

Prevalence and antimicrobial resistance of Shiga toxin-producing Escherichia coli in milk and dairy products in Egypt

Food contaminated with Shiga toxin-producing Escherichia coli (STEC) represents a hazardous public health problem worldwide. Therefore, the present study was performed to elucidate the virulent and antimicrobial resistance characteristics of STEC isolated from milk and dairy products marketed in Egypt. A total of 125 samples (raw market milk, bulk tank milk, Kareish cheese, white soft cheese, and small scale-produced ice cream, 25 each) were collected for determination the prevalence and antimicrobial resistance profiling of STEC. Thirty-six STEC isolates were recovered from milk and dairy products. Serological analysis illustrated that three isolates were E. coli O157:H7 and 33 isolates belonged to different serotypes. Molecular examination indicated that all isolates harboured stx1 and/or stx2 genes, 14 isolates expressed eaeA gene and 3 isolates possessed rfbE gene. Antimicrobial resistance profiling of the isolates was both phenotypically and genetically examined. Interestingly, 31 out of 36 (86.11%) isolates were multidrug-resistant and harboured the extended-spectrum β-lactamase encoding genes, namely, bla_CTX-M-15, bla_SHV-12 and bla_CTX-M-14. Moreover, 12 isolates (33.33%) harboured plasmid-mediated quinolone resistant gene, qnrS. The overall conclusion of the current investigation indicated insufficient hygienic measures adopted during milking, handling, and processing leading to development of pathogenic and multidrug-resistant STEC.

Genetic analysis of carbapenemase-producing Gram-negative bacteria isolated from a university teaching hospital in Egypt

A total of 65 non-replicate Gram-negative bacterial strains were recovered from clinical specimens between April and September 2014 at a University Hospital in Egypt. This collection was screened by PCR for carbapenemase-encoding genes, 16S rRNA methylases, and colistin resistance genes (mcr-1-mcr-8). Twenty-two strains (22/65, 33.8%) were positive for carbapenemase-encoding genes [13 NDM-1-producers (four Escherichia coli, two Klebsiella pneumoniae, and seven Providencia stuartii), two E. coli co-carrying NDM-5 and OXA-181, and seven Pseudomonas aeruginosa (three VIM-2, four VIM-24) strains]. The 16S rRNA methylase RmtC was detected in 12 NDM-1-producers for the first time in Egypt; no mcr genes were detected. A self-transmissible A/C plasmid was found to carry bla_NDM-1 in all NDM-1-producing strains. NDM-5 and OXA-181 were located on an untypeable and IncX3 plasmid, respectively. Additionally, Enterobacterial repetitive intergenic consensus (ERIC)-PCR revealed five clonally related P. stuartii isolates collected over a 1.5-month period. Thirteen carbapenemase-producing strains were isolated from burn patients who are at a high risk of developing infections and require special medical care. To our knowledge, this is the first report of NDM-1-producing-P. stuartii strains in an African burn unit, NDM-1- and RmtC-positive non-lactose fermenting E. coli globally, VIM-24-producing P. aeruginosa in Africa, and 16S RMTase rmtC-NDM-1-producers in Egypt. This work highlights the detection of different carbapenemase-producing bacterial strains within an Egyptian teaching hospital compromising the effectiveness of carbapenems and urgently asking the Egyptian medical authorities for implementation of antimicrobial surveillance plans and infection control policies to early detect and to effectively halt the rapid spread of these superbugs.

Understanding the Epidemiology of Multi-Drug Resistant Gram-Negative Bacilli in the Middle East Using a One Health Approach

In the last decade, extended-spectrum cephalosporin and carbapenem resistant Gram-negative bacilli (GNB) have been extensively reported in the literature as being disseminated in humans but also in animals and the environment. These resistant organisms often cause treatment challenges due to their wide spectrum of antibiotic resistance. With the emergence of colistin resistance in animals and its subsequent detection in humans, the situation has worsened. Several studies reported the transmission of resistant organisms from animals to humans. Studies from the middle east highlight the spread of resistant organisms in hospitals and to a lesser extent in livestock and the environment. In view of the recent socio-economical conflicts that these countries are facing in addition to the constant population mobilization; we attempt in this review to highlight the gaps of the prevalence of resistance, antibiotic consumption reports, infection control measures and other risk factors contributing in particular to the spread of resistance in these countries. In hospitals, carbapenemases producers appear to be dominant. In contrast, extended spectrum beta lactamases (ESBL) and colistin resistance are becoming a serious problem in animals. This is mainly due to the continuous use of colistin in veterinary medicine even though it is now abandoned in the human sphere. In the environment, despite the small number of reports, ESBL and carbapenemases producers were both detected. This highlights the importance of the latter as a bridge between humans and animals in the transmission chain. In this review, we note that in the majority of the Middle Eastern area, little is known about the level of antibiotic consumption especially in the community and animal farms. Furthermore, some countries are currently facing issues with immigrants, poverty and poor living conditions which has been imposed by the civil war crisis. This all greatly facilitates the dissemination of resistance in all environments. In the one health concept, this work re-emphasizes the need to have global intervention measures to avoid dissemination of antibiotic resistance in humans, animals and the environment in Middle Eastern countries.

Illumina short-read and MinION long-read WGS to characterize the molecular epidemiology of an NDM-1 Serratia marcescens outbreak in Romania

Background and Objectives

Serratia marcescens is an emerging nosocomial pathogen, and the carbapenemase bla_NDM has been reported in several surveys in Romania. We aimed to investigate the molecular epidemiology of S. marcescens in two Romanian hospitals over 2010–15, including a neonatal NDM-1 S. marcescens outbreak.

Methods

Isolates were sequenced using Illumina technology together with carbapenem-non-susceptible NDM-1-positive and NDM-1-negative Klebsiella pneumoniae and Enterobacter cloacae to provide genomic context. A subset was sequenced with MinION to fully resolve NDM-1 plasmid structures. Resistance genes, plasmid replicons and ISs were identified in silico for all isolates; an annotated phylogeny was reconstructed for S. marcescens. Fully resolved study NDM-1 plasmid sequences were compared with the most closely related publicly available NDM-1 plasmid reference.

Results

44/45 isolates were successfully sequenced (S. marcescens, n = 33; K. pneumoniae, n = 7; E. cloacae, n = 4); 10 with MinION. The S. marcescens phylogeny demonstrated several discrete clusters of NDM-1-positive and -negative isolates. All NDM-1-positive isolates across species harboured a pKOX_NDM1-like plasmid; more detailed comparisons of the plasmid structures demonstrated a number of differences, but highlighted the largely conserved plasmid backbones across species and hospital sites.

Conclusions

The molecular epidemiology is most consistent with the importation of a pKOX_NDM1-like plasmid into Romania and its dissemination amongst K. pneumoniae/E. cloacae and subsequently S. marcescens across hospitals. The data suggested multiple acquisitions of this plasmid by S. marcescens in the two hospitals studied; transmission events within centres, including a large outbreak on the Targu Mures neonatal unit; and sharing of the pKOX_NDM1-like plasmid between species within outbreaks.

High Prevalence of Antimicrobial Resistance in Gram-Negative Bacteria Isolated from Clinical Settings in Egypt: Recalling for Judicious Use of Conventional Antimicrobials in Developing Nations

This study was designed to investigate, at the molecular level, the antimicrobial resistance mechanisms of different antimicrobial resistance genes, including, extended-spectrum β-lactamases, AmpC β-lactamases, class 1 and 2 integrons, and plasmid-mediated quinolone resistance genes of Gram-negative bacteria isolated from clinical settings in Egypt. A total of 126 nonduplicate Gram-negative isolates were recovered from different clinical samples taken from hospitalized patients in Egypt in 2014. Antimicrobial susceptibility testing showed that, 93.6% (118/126) of the isolates had a multidrug-resistant phenotype. Interestingly, we reported a high level of antimicrobial resistance nearly for all tested antibiotics; to our knowledge, this is the first report from Egypt indicating very high level of antibiotic resistance in Egypt. Polymerase chain reaction screening and DNA sequencing revealed that, 75.4% (95/126) of the isolates harbored at least one extended-spectrum β-lactamase-encoding gene, with bla_CTX-M being the most prevalent (65.9%), followed by bla_SHV (46.8%). The AmpC β-lactamase, bla_CMY, was detected in 7.1% (9/126) of bacterial isolates, with bla_CMY-42 being the most prevalent. Class 1 integrons were detected in 50.8% (64/126) of the isolates, and class 2 integrons were detected in 2.4% (3/126) of the isolates. The plasmid-mediated quinolone resistance gene, qnr, was detected in 58.7% (74/126) of the tested isolates, with qnrS being the most prevalent. Several antimicrobial resistance determinants were identified in Egypt for the first time, such as SHV-27, SHV-28, SHV-33, SHV-63, SHV-71, SHV-82, SHV-142, CMY-42, CMY-6, and the new CMY-72 like. This study highlights the importance of the conscious use of conventional antimicrobials to overcome the multidrug resistance problem.

High frequency and molecular epidemiology of metallo-β-lactamase-producing gram-negative bacilli in a tertiary care hospital in Lahore, Pakistan

Background

Metallo-β-lactamase (MBL)-producing isolates have a strong impact on diagnostic and therapeutic decisions. A high frequency of MBL-producing gram-negative bacilli has been reported worldwide. The current study was based on determining the incidence of MBL-producing imipenem-resistant clinical isolates and investigating the β-lactamase gene variants in strains conferring resistance to a carbapenem drug (imipenem).

Methods

A total of 924 gram negative isolates were recovered from a tertiary care hospital in Lahore, Pakistan, during a two-year period (July 2015 to February 2017). The initial selection of bacterial isolates was based on antibiotic susceptibility testing. Strains resistant to imipenem were processed for the molecular screening of β-lactamase genes. Statistical analysis for risk factor determination was based on age, gender, clinical specimen and type of infection.

Results

The rate of imipenem resistance was calculated to be 56.51%. Among the 142 strains processed, the phenotypic tests revealed that the incidence of MBLs was 63.38% and 86.61% based on the combination disc test and the modified Hodge test, respectively. The frequencies of bla_TEM, bla_SHV,bla_OXA,bla_IMP-1, and bla_VIM genes were calculated to be 46%, 34%, 24%, 12.5% and 7%, respectively. The co-expression of bla_MBL (bla_IMP and bla_VIM) and bla_ESBL (bla_TEM, bla_SHV,bla_OXA) was also detected through multiplex and singleplex PCR. bla_OXA, bla_TEM and bla_SHV coexisted in 82% of the isolates. Co-expression of ESBL and MBL genes was found in 7% of the isolates.

Conclusion

To our knowledge, this is the first report from Pakistan presenting the concomitant expression of bla_OXA, bla_TEM and bla_SHV with bla_IMP-1 and bla_VIM in MBL-producing gram-negative bacilli.

Carbapenem resistance among clinical and environmental Gram-negative isolates recovered from hospitals in Gaza strip, Palestine

Background

The world is threatened by the ongoing emergence of carbapenem resistant organisms, which are contributing to increasing morbidity and mortality rates. The main objective of this study was to highlight carbapenem resistance among clinical and environmental Gram-negative bacteria (GNB) isolates.

Methods

A cross-sectional study wherein 210 clinical isolates, 150 environmental swabs, and 110 air samples were collected from three major hospitals in Gaza strip: Al-Shifa, AlNaser and the European Gaza hospitals. The study lasted for seven months (September 2016 to March 2017). All isolates/samples were cultured and identified using conventional bacteriological methods. All GNB isolates were tested for their antimicrobial susceptibility using the disk diffusion method. Modified Hodge Test (MHT) was performed to investigate carbapenemases production.

Results

The overall percentage of carbapenem resistance among GNB was (30/247) 12.1%. Resistance to imipenem was (20/247) 8.1% while resistance to ertapenem and meropenem was (8/226) 3.5% and (2/247) 0.8%, respectively. The intensive care units exhibited the highest resistance rate 9/17 (52.9%). Carbapenem resistance among Enterobacteriaceae was (30/226) 13.2% while in Pseudomonas it was (0/21) 0%. Klebsiella spp. was the most resistant to carbapenems 13/90 (14.4%), followed by E. coli (9/91) 9.8%. Seven isolates out of 30 (23.3%) were positive for MHT. All Enterobacteriaceae isolates had a multiple antibiotic resistance (MAR) index higher than 0.2, while those of Pseudomonas had an average of 0.2. GNB were isolated from 19/110 (17.2%) and 21/150 (14%) of air and environmental samples, respectively.

Conclusion

The resistance found, after a recent introduction of carbapenem use in Gaza, shows the need for policies to prevent misuse and overuse of carbapenems, the need for infection control procedures and screening policies for carbapenem resistance on a routine basis.

Global antimicrobial resistance in Gram-negative pathogens and clinical need

Resistance in Gram-negative bacteria has become a serious problem in many regions of the world as it may reduce the treatment options substantially. Carbapenem-resistance is a good marker for such situations and is most prevalent in Acinetobacter, Pseudomonas but also increasingly in Enterobacteriaceae, especially Klebsiella. This review gives a rough global picture highlighting the epicentres of resistance. The medical need for novel treatment options globally is undeniable even if many countries with good stewardship and infection control conditions are not highly affected. Antibiotic pipelines are encouraging, as new drugs in development reduce the resistance rate to individual pathogens. Despite some progress, efforts to discover and develop novel drugs that are not prone to cross-resistance to existing antibiotic classes should be intensified.

OXA-48-like carbapenemases producing Enterobacteriaceae in different niches

The emergence of carbapenem-resistant enterobacterial species poses a serious threat to public health worldwide. OXA-48-type carbapenem-hydrolyzing class D β-lactamases are widely distributed among Enterobacteriaceae, with significant geographical differences. To date, 11 OXA-48-like variants have been identified, with classical OXA-48 being the most widespread. These enzymes show high-level hydrolytic activity against penicillins and low-level hydrolysis towards carbapenems. Since the first description of the OXA-48 carbapenemase in Turkey, bacterial strains producing the enzyme have been extensively reported in nosocomial and community outbreaks in many parts of the word, particularly in the Mediterranean area and European countries. The rapid spread of Enterobacteriaceae producing OXA-48-like enzymes in different ecosystems has become a serious issue recently. The number of reservoirs for such organisms is increasing, not only in hospitals, but also in the community, among animals (e.g., livestock, companion animals, and wildlife) and in the environment. This review aims to summarize the main characteristics of the OXA-48-type carbapenemases, covering genetic and enzymatic traits, their epidemiology, clonality and associated genes, correlation with extended-spectrum β-lactamases (ESBLs) or plasmidic AmpC (pAmpC) in different bacterial species worldwide.