Whole Genome Sequence Analysis of Multidrug Resistant Escherichia coli and Klebsiella pneumoniae Strains in Kuwait

The spread of carbapenem-resistant Escherichia coli and Klebsiella pneumoniae is a global concern. The management of infections caused by multidrug resistance (MDR) isolates poses substantial clinical challenges in both hospitals and communities. This study aimed to investigate the genetic characteristics and variations of MDR E. coli and K. pneumoniae isolates. Bacterial identification and antibiotic susceptibility testing against 19 antibiotics were performed by standard methods. Whole genome sequencing (WGS) was carried out on eight carbapenem-resistant isolates using an Illumina MiSeq platform. The assembled draft genomes were annotated, then sequences were blasted against antimicrobial resistance (AMR) genes database. WGS detected several resistance genes mediating the production of β-lactamases, including carbapenems and extended-spectrum β-lactamase genes as (bla_OXA-1/-48, bla_KPC-2/-29, bla_CMY-4/-6, bla_SHV-11/-12, bla_TEM-1, bla_CTX-M-15, bla_OKP-B, bla_ACT and bla_EC). Furthermore quinolone resistance including oqxA/oqxB, aac(6′)-Ib-cr5, gyrA_D87N, gyrA_S83F, gyrA_S83L, parC_S80I, parE_S458A, parE_I355T, parC_S80I, and qnrB1. In addition to aminoglycoside modifying enzymes genes (aph(6)-Id, aph(3″)-Ib, aac(3)-IIa, aac(6′)-Ib, aadA1, aadA2 and aadA5), trimethoprim-sulfamethoxazole (dfrA12/A14/A17 and sul1/sul2), tetracycline (tetA and tetB), fosfomycin (fosA and uhpT_E350Q) resistance genes, while other genes were detected conferring chloramphenicol (floR, catA2, and efflux pump cmIA5), macrolides resistance (mph(A) and erm(B), and quaternary ammonium efflux pump qacEdelta. Bleomycin and colistin resistance genes were detected as ble and pmrB_R256G, respectively. Comprehensive analysis of MDR strains provided by WGS detected variable antimicrobial resistance genes and their precise resistance mechanism. WGS is essential for control and prevention strategies to combat the growing threat of AMR and the implementation of multifaceted interventions are needed.

Emerging Status of Multidrug-Resistant Bacteria and Fungi in the Arabian Peninsula

Simple Summary

The incidence and developing status of multidrug-resistant bacteria and fungi, as well as their related mortality, is reviewed by a systematic published literature search from nine countries in the Arabian Peninsula. In order to analyse the emerging status and mortality, a total of 382 research articles were selected from a comprehensive screening of 1705 papers. More than 850 deaths reported since 2010 in the Arabian Peninsula due to the infection of multidrug-resistant bacteria and fungi. Multidrug-resistant bacteria Acinetobacter baumannii, Mycobacterium tuberculosis, Staphylococcus aureus, and fungi Candida auris are the most prevalent and causing high deaths. To control these infections and associated deaths in the Arabian Peninsula, continuous preventive measures, accurate methods for early diagnosis of infection, active surveillance, constant monitoring, developing vaccines, eradicating multidrug resistance modulators, and data sharing among countries are required.

Abstract

We aimed to identify the prevalence and emerging status of multidrug-resistant bacteria and fungi and their associated mortality in nine countries in the Arabian Peninsula. Original research articles and case studies regarding multidrug-resistant bacteria and fungi in the Arabian Peninsula, published during the last 10 years, were retrieved from PubMed and Scopus. A total of 382 studies were included as per the inclusion and exclusion criteria, as well as the PRISMA guidelines, from a thorough screening of 1705 articles, in order to analyse the emerging status and mortality. The emerging nature of >120 multidrug-resistant (MDR) bacteria and fungi in the Arabian Peninsula is a serious concern that requires continuous monitoring and immediate preventive measures. More than 50% (n = 453) of multidrug-resistant, microbe-associated mortality (n = 871) in the Arabian Peninsula was due to MDR Acinetobacter baumannii, Mycobacterium tuberculosis and Staphylococcus aureus infection. Overall, a 16.51% mortality was reported among MDR-infected patients in the Arabian Peninsula from the 382 articles of this registered systematic review. MDR A. baumannii (5600 isolates) prevailed in all the nine countries of the Arabian Peninsula and was one of the fastest emerging MDR bacteria with the highest mortality (n = 210). A total of 13,087 Mycobacterium tuberculosis isolates were reported in the region. Candida auris (580 strains) is the most prevalent among the MDR fungal pathogen in the Arabian Peninsula, having caused 54 mortalities. Active surveillance, constant monitoring, the development of a candidate vaccine, an early diagnosis of MDR infection, the elimination of multidrug resistance modulators and uninterrupted preventive measures with enhanced data sharing are mandatory to control MDR infection and associated diseases of the Arabian Peninsula. Accurate and rapid detection methods are needed to differentiate MDR strain from other strains of the species. This review summarises the logical relation, prevalence, emerging status and associated mortality of MDR microbes in the Arabian Peninsula.

Comparative Study of CTX-M-15 Producing Escherichia coli ST131 Clone Isolated from Urinary Tract Infections and Acute Diarrhoea

Background and Purpose

The alarming increase in the prevalence of CTX-M-15 extended-spectrum β-lactamase (ESBL) producing E. coli has been significantly linked to the clonal expansion of emerging sequence type (ST131). This study aimed to screen for the O16/O25-ST131 clones among different phylogenetic types of E. coli strains isolated from urinary and diarrhoeal samples.

Methods

A total of 205 E. coli strains isolated from patients with UTI and acute diarrhoea were investigated by phenotypic and genotypic methods for ESBL identification. Molecular methods were used for identification of O25/O16-ST131 clone and phylogenetic typing of E. coli isolates.

Results

O25-ST131 clone was detected in 89/105 (84.8%) and 47/100 (47%) of urinary and intestinal E. coli isolates, respectively, with a significant difference (P-value<0.001). There was a significant high rate of occurrence of ESBLs, MDR, and antibiotic resistance to most antibiotic classes among O25-ST131 than non-O25-ST131 isolates. CTX-M-15 gene was detected in 64/71 (90%) of ESBLs producing intestinal isolates and 54/79 (68.4%) of urinary ESBLs producing isolates. The O25-ST131 clone was reported among all phylogenetic groups. The O16-ST131 clone serotype was not detected in the study isolates.

Conclusion

High prevalence of the O25-ST131 clone was reported among extraintestinal and intestinal E. coli isolates. First detection of the O25-ST131 clone among phylogenetic groups other than group B2 draws attention of the ability of this clone to transfer among commensal groups. An increasing in the prevalence of CTX-M-15 among E. coli strains especially of intestinal origin is alarming as the intestine is the main reservoir for ExPEC strains causing UTI.

Prevalence of antibiotic-resistant organisms among hospitalized patients at a tertiary care center in Lebanon, 2010-2018

BACKGROUND

Infections due to antibiotic resistant organisms (ARO) among hospitalized patients are associated with increased morbidity, mortality, and healthcare costs. Longitudinal data about antimicrobial resistance are scarce in Lebanon and the region. The objective of this study is to describe the temporal trends of resistance of selected pathogens among hospitalized patients at a tertiary care center in Lebanon.

METHODS

We conducted a retrospective review of surveillance data from 2010 until 2018. Six target organisms isolated from hospitalized patients were included: carbapenem-resistant Escherichia coli (CREC), carbapenem-resistant Klebsiella spp. (CRKP), multi-drug resistant Pseudomonas aeruginosa (MDRPA), carbapenem-resistant Acinetobacter baumannii (CRAB), methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant Enterococcus spp. (VRE). Correlation analysis was performed to evaluate for temporal trends.

RESULTS

A total of 15,901 isolates were examined, most of which were obtained from urinary specimens. Among Gram-negative organisms, the highest resistance was found among CRAB (81.7%), followed by CRKP (6.5%) and CREC (3.3%). MDRPA overall prevalence was 0.8%. Among Gram-positive organisms, the prevalence of MRSA and VRE was 26.2% and 2.6%, respectively. CREC, MRSA, and VRE showed statistically significant increasing temporal trends, while CRAB decreased significantly from 2013 to 2018.

CONCLUSION

These data are helpful in characterizing the epidemiology of antimicrobial resistance in Lebanon and show that controlling emerging resistance is achievable with concerted infection control and antimicrobial stewardship efforts. Caution should be exercised to contain early on the spread of CREC and of resistant Gram-positive pathogens.

Antimicrobial resistance among GLASS pathogens in conflict and non-conflict affected settings in the Middle East: a systematic review

BACKGROUND

In spite of the evident general negative effects of armed conflict on countries' health systems and populations' health outcomes, little is known about similar impacts of conflicts on the spread of antimicrobial resistances (AMR). This review was to address this evidence gap and describe: 1. Patterns of AMR in the Middle East (ME) and resistance profiles of pathogens included in the Global AMR Surveillance System (GLASS) supported by the World Health Organization; 2. Differences in proportions of AMR isolates between conflict and non-conflict countries.

METHODS

A systematic literature review was conducted following PRISMA guidelines and searching five electronic databases. Subject heading and free text were searched for "antimicrobial resistances" and "Middle East", to identify observational studies on AMR published from January 2011 to June 2018. Data were extracted from included articles on a predefined set of variables. Percentages of AMR were analysed as median and interquartile ranges. Risk of bias was assessed using the Newcastle-Ottawa Scale.

RESULTS

A total of 132 articles met the inclusion criteria. Included studies showed heterogeneity in study design, laboratory methods and standards for interpretation of results, and an overall high risk of bias. Main findings were the following: 1. High proportions of carbapenem resistance in Acinetobacter spp. (median 74.2%), and both carbapenem resistance (median 8.1 and 15.4% for E. coli and K. pneumoniae respectively) and ESBL-production (median 32.3 and 27.9% for E. coli and K. pneumoniae respectively) amongst Enterobacteriaceae. S. aureus isolates showed a median methicillin resistance percentage of 45.1%, while vancomycin resistance was almost absent. A median of 50% of the strains of S. pneumoniae showed non-susceptibility to penicillin. 2. Similar trends were observed in conflict and non-conflict affected countries.

CONCLUSIONS

There is a lack of standardization in the methodological approach to AMR research in the Middle East. The proportion of antibiotic resistances among specific GLASS pathogens is high, particularly among Acinetobacter spp.

Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in cattle production - a threat around the world

Food producing animal is a global challenge in terms of antimicrobial resistance spread. Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae are relevant opportunistic pathogens that may spread in many ecological niches of the One Health approach as human, animal and environment due to intestinal selection of antimicrobial resistant commensals in food production animals. Cattle production is a relevant ecological niche for selection of commensal bacteria with antimicrobial resistance from microbiota. Enterobacteriaceae show importance in terms of circulation of resistant-bacteria and antimicrobial resistance genes via food chain creating a resistance reservoir, setting up a threat for colonization of humans and consequent health risk. ESBL-producing Enterobacteriaceae are a threat in terms of human health responsible for life threatening outbreaks and silent enteric colonization of community populations namely the elder population. Food associated colonization is a risk difficult to handle and control. In a time of globalization of food trading, population intestinal colonization is a mirror of food production and in that sense this work aims to make a picture of ESBL-producing Enterobacteriaceae in animal production for food over the world in order to make some light in this reality of selection of resistant threats in food producing animal.

Urinary tract infection caused by extended-spectrum β-lactamase-producing bacteria: Risk factors and antibiotic resistance

BACKGROUND

The aim of this study was to investigate the risk factors for acquisition of extended spectrum β-lactamase (ESBL)-producing bacteria in community-acquired urinary tract infection (UTI) and to evaluate their antimicrobial resistance.

METHODS

The medical records of hospitalized children were retrospectively evaluated. Children with ESBL-producing bacteria UTI were matched with controls with non-ESBL-producing bacteria UTI of the same age and gender.

RESULTS

A total of 243 patients with community-acquired UTI in a 5 year period were evaluated, of whom 46% had UTI caused by ESBL bacteria. Seventy-seven cases were matched with 77 controls. There were no significant differences in the clinical presentation between the two groups apart from a longer hospital stay in the ESBL group (9.1 ± 5.5 days vs 8.0 ± 4.4 days, P = 0.013). Significant potential risk factors for ESBL-UTI were previous use of antibiotics in the last 3 months, previous hospitalization in the last 3 months, history of recurrent UTI, and presence of renal anomalies. On logistic regression analysis, history of previous hospitalization in the last 3 months (OR, 3.83; 95%CI: 1.49-9.84) was identified as an independent significant risk factor for ESBL-UTI. There was a significantly higher resistance to amoxicillin-clavulanate, amikacin, gentamycin and quinolones in the ESBL group compared with the control group.

CONCLUSION

Recognizing the risk factors for ESBL-UTI helps to identify the high-risk cases and enables proper management.

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.

Prevalence of quinolone-resistant uropathogenic Escherichia coli in a tertiary care hospital in south Iran

Background: Quinolones are a family of synthetic antimicrobial agents with a broad antibacterial activity commonly used as a suitable therapy in patients with urinary tract infection (UTI). In the present study, we aimed to evaluate the prevalence of quinolones resistance and the presence of plasmid-mediated quinolone resistance (PMQR) genes among Escherichia coli isolates.

Methods

This study was performed on a collection of 121 E. coli isolates derived from patients with UTI. Antimicrobial susceptibility to nalidixic acid, ciprofloxacin, levofloxacin, norfloxacin, and ofloxacin was specified by the disk diffusion method. The presence of PMQR genes was determined by PCR method.

Results

Antibiotic susceptibility results showed that the highest and lowest resistance rates were against nalidixic acid (71.9%) and norfloxacin (44.6%), respectively. The molecular results showed that 40 (33.1%) and 15 (12.4%) of the isolates were positive for qnrS and qnrB genes, respectively. Meanwhile, 5 (4.1%) of the isolates were found positive for both genes, while none were found to be positive for qnrA gene. There was no significant association between the presence of qnr genes and higher antibiotic resistance.

Conclusion

We found high levels of quinolones resistance (more than 40%) among E. coli strains isolated from patients with UTIs in the south of Iran. We further report the prevalence of PMQR genes among uropathogenic E. coli; however, it seems that these genes are not the main components of quinolone resistance in our region.

Investigating possible association between multidrug resistance and isolate origin with some virulence factors of Escherichia coli strains isolated from infant faeces and fresh green vegetables

AIMS

In this study, the association between multidrug resistance (MDR) and the expression of some virulence factors were evaluated in Escherichia coli strains isolated from infant faeces and fresh green vegetables. The effect of isolate origin on associated virulence factors was evaluated. In addition, genetic fingerprinting of a sample of these isolates (10 isolates from each group) was studied in order to detect any genetic relatedness among these isolates.

METHODS AND RESULTS

Escherichia coli isolates were divided into four groups based on their origin (human faeces or plant) and their antibiotic resistance (multiresistance or susceptible). PCR was used to investigate heat-labile and heat-stable enterotoxin genes, and four siderophore genes (aerobactin, enterobactin, salmochelin and yersiniabactin). Genetic fingerprinting of the isolates was performed using enterobacterial repetitive intergenic consensus PCR. Siderophore production was measured by a colorimetric method. Biofilm formation was evaluated by a crystal violet assay. The results of the study showed that the expression of MDR is not significantly associated with an increase in these virulence factors or with biofilm formation. However, the origin of isolates had a significant association with siderophore gene availability and consequently on the concentrations of siderophores released. Genetic fingerprinting indicated that human and plant isolates have the same clonal origin, suggesting their circulation among humans and plants.

CONCLUSION

Antibiotic-susceptible strains of E. coli may be as virulent as MDR strains. Results also suggest that the environment can play a potential role in selection of strains with specific virulence factors.

SIGNIFICANCE AND IMPACT OF THE STUDY

Antibiotic-susceptible isolates of Escherichia coli from plant or human origin can be as virulent as the multidrug resistance (MDR) ones. Genetic relatedness was detected among the isolates of plant and human origin, indicating the circulation of these bacteria among human and plants. This could imply a potential role for environmental antimicrobial resistant bacteria in human infection.

Epidemiology of common resistant bacterial pathogens in the countries of the Arab League

No uniformly organised collection of data regarding antimicrobial resistance has occurred in the countries of the Arab League. 19 countries of the Arab League have published data for antimicrobial susceptibility for the WHO priority organisms, and seven of 14 of these organisms are included in this Review (Escherichia coli, Klebsiella spp, Pseudomonas aeruginosa, Acinetobacter baumannii, Salmonella spp, Staphylococcus aureus, and Streptococcus pneumoniae). Although E coli and Klebsiella spp resistance to third-generation cephalosporins is common in all countries, with prevalence reaching more than 50% in Egypt and Syria, carbapenem resistance is emerging, albeit with a prevalence of less than 10%. Conversely, a large amount of carbapenem resistance has been reported for P aeruginosa and A baumannii across the Arab League, reaching 50% and 88% of isolates in some countries. As for Salmonella spp, the prevalence of fluoroquinolone resistance has exceeded 30% in several areas. With regards to the Gram-positive pathogens, the prevalence of meticillin resistance in S aureus is reported to be between 20% and 30% in most countries, but exceeds 60% in Egypt and Iraq. The prevalence of penicillin non-susceptibility among pneumococci has reached more than 20% in Algeria, Egypt, Morocco, Saudi Arabia, and Tunisia. These findings highlight the need for structured national plans in the region to target infection prevention and antimicrobial stewardship.

Multiple drug resistance and biocide resistance in Escherichia coli environmental isolates from hospital and household settings

Background

Antibiotic resistance of environmental Escherichia coli in hospitals could be increased due to extensive use of biocides resulting in serious infections. In this study, the prevalence of antibiotic resistance of environmental isolates of E. coli from hospitals and household settings were evaluated and compared. In addition, the association between biocide minimum inhibitory concentration (MIC) and multiple drug resistance (MDR) was investigated.

Methods

Environmental samples were collected from different homes and hospitals in Amman, Jordan. The isolates were identified phenotypically and by PCR. Antibiotic susceptibility tests and MIC of selected biocides were performed on the isolates. Screening for blaCTX-M group 1 was also performed.

Results

Of 21 E. coli strains isolated, 47.6% were MDR and 67.9% were phenotypically identified as extended spectrum beta-lactamase (ESBL) producers. The occurrence of these ESBL isolates was comparable between household and hospital settings (P > 0.05). The MIC values of the biocides tested against all isolates were well below the in-use concentration of biocides. Moreover, the MICs of biocides were comparable between isolates from households and those from hospitals (P > 0.05). No association was found between MDR and biocide MIC (P > 0.05). Most of ESBL isolates harboured blaCTX-M 1.

Conclusions

The extensive use of biocides in hospitals is not associated with MDR nor does it affect the MIC of biocides against E.coli.

Molecular Characterization of Multidrug Resistant Uropathogenic E. Coli Isolates from Jordanian Patients

Background

Emergence of multi-drug resistant uropathogenic E. coli strains is an increasing problem to empirical treatment of urinary tract infections in many countries. This study investigated the magnitude of this problem in Jordan.

Methods

A total of 262 E. coli isolates were recovered from urine samples of Jordanian patients which were suspected to have urinary tract infections (UTIs). All isolates were primarily identified by routine biochemical tests and tested for antimicrobial susceptibility by disc diffusion method. Fifty representative Multidrug Resistance (MDR) E. coli isolates to 3 or more antibiotic classes were tested for the presence of resistance genes of blaCTX-M- 1, 9 and 15, carbapenemase (blaIMP, blaVIM, blaNDM-1, blaOXA-48), fluoroquinolones mutated genes (parC and gyrA) and clone of ST131 type using PCR methods.

Results

A total of 150/262 (57.3%) of E. coli isolates were MDR. Urine samples of hospitalized patients showed significantly more MDR isolates than outpatients. Fifty representative MDR E. coli isolates indicated the following molecular characteristics: All were positive for mutated parC gene and gyrA and for ST131 clone, and 78% were positive for genes of CTX-M-15, 76% for CTX-M-I and for 8% CTX-M-9, respectively. Additionally, all 50 MDR E. coli isolates were negative for carbapenemase genes (blaIMP, blaVIM, blaNDM-1, blaOXA-48), except of one isolate was positive for blaKPC-2 .

Conclusion

This study indicates alarming high rates recovery of MDR uropathogenic E. coli from Jordanian patients associated with high rates of positive ST131 clone, fluoroquinolone resistant and important types of blaCTX-M.

Epidemiological Features of Clostridium difficile Colonizing the Intestine of Jordanian Infants

Clostridium difficile is commonly found in the intestine of infants without causing any disease. This study investigated the most important epidemiological features of C. difficile strains colonizing intestine of Jordanian infants. A total of 287 fecal samples were collected from infants admitted to the Jordan University Hospital (JUH) over the period of 2015. Samples were cultured for C. difficile and their growth was identified using microbiological culture and PCR. The overall C. difficile colonization rate among hospitalized and nonhospitalized infants was 37/287 (12.9%). Neonates were less colonized than other infants (8.7% verses 19.5%). Colonization of the infants with C. difficile toxigenic strains (TcdA and TcdB) was observed in 54% of the isolates, whereas those colonized with nontoxigenic strains were 46% and only one isolate was positive for binary toxin. Breast feeding of infants is a significant factor associated with decreased colonization with C. difficile. All C. difficile strains were susceptible to vancomycin and metronidazole, while high resistance rate to ciprofloxacin (78.4%) and less resistance rate to erythromycin (29.7%) were detected among the isolates. The results showed that 40.5% of the isolates carried mutated gyrA and gyrB genes which have cross-resistance to ciprofloxacin and moxifloxacin. This study represents useful epidemiological features about C. difficile colonizing intestine of infants living in a developing country.