Molecular characterization of extended spectrum β -lactamases enterobacteriaceae causing lower urinary tract infection among pediatric population

Occurrence and molecular characteristics of antimicrobial resistance, virulence factors, and extended-spectrum β-lactamase (ESBL) producing Salmonella enterica and Escherichia coli isolated from the retail produce commodities in Bangkok, Thailand

The incidence of antimicrobial resistance (AMR) in the environment is often overlooked and leads to serious health threats under the One Health paradigm. Infection with extended-spectrum β-lactamase (ESBL) producing bacteria in humans and animals has been widely examined, with the mode of transmission routes such as food, water, and contact with a contaminated environment. The purpose of this study was to determine the occurrence and molecular characteristics of resistant Salmonella enterica (S. enterica) (n = 59) and Escherichia coli (E. coli) (n = 392) isolated from produce commodities collected from fresh markets and supermarkets in Bangkok, Thailand. In this study, the S. enterica isolates exhibited the highest prevalence of resistance to tetracycline (11.9%) and streptomycin (8.5%), while the E. coli isolates were predominantly resistant to tetracycline (22.5%), ampicillin (21.4%), and sulfamethoxazole (11.5%). Among isolates of S. enterica (6.8%) and E. coli (15.3%) were determined as multidrug resistant (MDR). The prevalence of ESBL-producing isolates was 5.1% and 1.0% in S. enterica and E. coli, respectively. A minority of S. enterica isolates, where a single isolate exclusively carried blaCTX-M-55 (n = 1), and another isolate harbored both blaCTX-M-55 and blaTEM-1 (n = 1); similarly, a minority of E. coli isolates contained blaCTX-M-55 (n = 2) and blaCTX-M-15 (n = 1). QnrS (11.9%) and blaTEM (20.2%) were the most common resistant genes found in S. enterica and E. coli, respectively. Nine isolates resistant to ciprofloxacin contained point mutations in gyrA and parC. In addition, the odds of resistance to tetracycline among isolates of S. enterica were positively associated with the co-occurrence of ampicillin resistance and the presence of tetB (P = 0.001), while the E. coli isolates were positively associated with ampicillin resistance, streptomycin resistance, and the presence of tetA (P < 0.0001) in this study. In summary, these findings demonstrate that fresh vegetables and fruits, such as cucumbers and tomatoes, can serve as an important source of foodborne AMR S. enterica and E. coli in the greater Bangkok area, especially given the popularity of these fresh commodities in Thai cuisine.

Application of Antimicrobial Peptides as Diagnostic Biosensors

The COVID-19 pandemic has shown how emerging infectious diseases could quickly affect the global health and economy. New pathogens with pandemic potential are also expected to appear soon. Moreover, the large use of antibiotics has led to the development of different so-called "superbugs" capable of escaping all of the current antibiotics. In this context, the early and cost-effective detection of pathogens is crucial to avoid the spreading of new pathogens. Here, we present molecular sensors for the recognition of a broad panel of different bacterial species. The detection is based on the use of bacteria-binding peptides (BBPs) in combination with horseradish peroxidase (HRP). We developed a reliable ELISA-like assay that permits us to study the affinity of different BBPs toward some of the most important bacterial pathogens.

A multicentre study to determine the in vitro efficacy of flomoxef against extended-spectrum beta-lactamase producing Escherichia coli in Malaysia

Background

The high burden of extended-spectrum beta-lactamase-producing (ESBL)-producing Enterobacterales worldwide, especially in the densely populated South East Asia poses a significant threat to the global transmission of antibiotic resistance. Molecular surveillance of ESBL-producing pathogens in this region is vital for understanding the local epidemiology, informing treatment choices, and addressing the regional and global implications of antibiotic resistance.

Methods

Therefore, an inventory surveillance of the ESBL-Escherichia coli (ESBL-EC) isolates responsible for infections in Malaysian hospitals was conducted. Additionally, the in vitro efficacy of flomoxef and other established antibiotics against ESBL-EC was evaluated.

Results

A total of 127 non-repetitive ESBL-EC strains isolated from clinical samples were collected during a multicentre study performed in five representative Malaysian hospitals. Of all the isolates, 33.9% were isolated from surgical site infections and 85.8% were hospital-acquired infections. High rates of resistance to cefotaxime (100%), cefepime (100%), aztreonam (100%) and trimethoprim-sulfamethoxazole (100%) were observed based on the broth microdilution test. Carbapenems remained the most effective antibiotics against the ESBL-EC, followed by flomoxef. Antibiotic resistance genes were identified by PCR. The blaCTX-M-1 was the most prevalent ESBL gene, with 28 isolates (22%) harbouring blaCTX-M-1 only, 27 isolates (21.3%) co-harbouring blaCTX-M-1 and blaTEM, and ten isolates (7.9%) co-harbouring blaCTX-M-1, blaTEM and blaSHV. A generalised linear model showed significant antibacterial activity of imipenem against different types of infection. Besides carbapenems, this study also demonstrated a satisfactory antibacterial activity of flomoxef (81.9%) on ESBL-EC, regardless of the types of ESBL genes.

Detection of extended-spectrum β-lactamase-producing Escherichia coli genes isolated from cat rectal swabs at Surabaya Veterinary Hospital, Indonesia

Background and Aim

Escherichia coli causes a bacterial illness that frequently affects cats. Diseases caused by E. coli are treated using antibiotics. Because of their proximity to humans, cats possess an extremely high risk of contracting antibiotic resistance genes when their owners touch cat feces containing E. coli that harbor resistance genes. This study was conducted to identify multidrug-resistant E. coli and extended-spectrum β-lactamase (ESBL)-producing genes from cat rectal swabs collected at Surabaya City Veterinary Hospital to determine antibiotic sensitivity.

Materials and Methods

Samples of cat rectal swabs were cultured in Brilliant Green Bile Lactose Broth medium and then streaked on eosin methylene blue agar medium for bacterial isolation, whereas Gram-staining and IMViC tests were conducted to confirm the identification results. The Kirby-Bauer diffusion test was used to determine antibiotic sensitivity, and the double-disk synergy test was used to determine ESBL-producing bacteria. Molecular detection of the genes TEM and CTX-M was performed using a polymerase chain reaction.

Results

Based on morphological culture, Gram-staining, and biochemical testing, the results of sample inspection showed that of the 100 cat rectal swab samples isolated, 71 (71%) were positive for E. coli. Furthermore, 23 E. coli isolates (32.39%) demonstrated the highest resistance to ampicillin. Four isolates were confirmed to be multidurg-resistant and ESBL-producing strains. Molecular examination revealed that three E. coli isolates harbored TEM and CTX-M.

Conclusion

In conclusion, pet owners must be educated on the use of antibiotics to improve their knowledge about the risks of antibiotic resistance.

Urinary tract infections in children from the Gulf Cooperation Council countries: a literature review (2011-2022)

Urinary tract infections (UTIs) are common healthcare-associated and community-acquired bacterial infections in children. Data on pediatric UTIs in the Gulf Cooperation Council (GCC) region (Bahrain, Kuwait, Oman, Qatar, Saudi Arabia, and the United Arab Emirates) have not been collated. Our aim is to review the published literature on the risk factors, etiology, antimicrobial susceptibility, and treatment of pediatric (aged <18 years) UTIs from healthcare and community settings in the GCC countries.

Antibiotic use in infants within the first year of life is associated with the appearance of antibiotic-resistant genes in their feces

Background

Antibiotic resistance, an increasing challenge, is not only a national threat but also a global threat. Carriage of resistance genes is not limited to adults alone, various microbiota niches present in the body system of children have been found to harbor bacteria carrying resistant genes, especially, their gut microbiota. This study aims to identify selected antibiotic-resistant genes from the fecal samples of infants and the association of antibiotics use with the occurrence of resistant genes in the infant's gut.

Methods

A total number of 172 metagenomic DNA samples previously extracted from stool samples of 28 Nigerian babies longitudinally within their first year of life were screened for the presence of ESBL genes (blaSHV, blaTEM, and blaCTX-M), PMQR genes (qnrA, qnrB, qnrS, qepA), ribosomal protection protein tetracycline resistance gene, (RPP) β-lactamase (blaZ), macrolide (ermA, ermB, mefA/E), aminoglycoside modifying enzymes gent^R (aac(6')/aph(2″)) and dfrA genes by PCR. Nineteen (19) of the 28 babies used antibiotics during the study. The association between antibiotic use by the babies within the first year of life and occurrence of resistant genes were analyzed by Spearman rank correlation.

Results

One hundred and twenty-two (122) samples (71%) out of the 172 isolates had antibiotic-resistance genes. PMQR genes were absent in all the samples. Three isolates had blaTEM gene, nine isolates had blaSHV gene, six isolates had blaCTX-M gene and 19 isolates had dfrA gene, 31 samples had tet gene, 29 samples had mef gene, 27 samples had ermB gene, four samples had ermA gene, 13 samples had blaZ gene and 16 samples had aac gene. The babies whose samples had resistant genes used antibiotics in the same months the samples were collected. Interestingly, the 11 babies whose samples had the dfrA gene all used antibiotics in the same months their samples were collected but none of them used trimethoprim/sulfamethoxazole antibiotic. The overall correlation matrix of the babies showed a strong association between antibiotic use (AU) and antibiotic use presence of resistance genes (AUPRG) with a coefficient of 0.89. Antibiotic-resistant genes are present in the gut of infants and their occurrence is strongly connected with antibiotic use by infants.

Drug resistance and susceptibility of amikacin in children with extended-spectrum beta-lactamase-producing Enterobacterales: a systematic review with meta-analysis

Antibiotic resistance surveillance may be essential to identify patterns of antibiotic resistance and guide treatment choices. Therefore, this systematic review and meta-analysis aimed to evaluate amikacin resistance and susceptibility in children with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE). From inception to September 5, 2022, relevant studies were searched via PubMed, Embase, Cochrane Library, and Web of Science databases. A network meta-analysis was conducted to explore the sequencing of resistance rates in amikacin and other antibiotics. Totally, 26 studies with 2582 clusters of bacterial isolates were included. The resistance rate of amikacin in children with ESBL-PE was 10.1%, higher than the resistance rate of tigecycline (0.0%), ertapenem (0.4%), meropenem (0.7%), and imipenem (3.0%). For the drug susceptibility rate in children with ESBL-PE, the susceptibility rate of amikacin (89.7%) was lower than tigecycline (99.6%), imipenem (96.8%), meropenem (97.3%), and ertapenem (95.6%). Amikacin showed a low drug resistance and a high drug resistance in children with ESBL-PE infection, making it a good option for the treatment of the infection caused by ESBL-PE.

Clonal groups of extended-spectrum β-lactamase and biofilm producing uropathogenic Escherichia coli in Iran

Pathogenicity of a bacterium is affected by the social characteristics of the population and environmental factors. The ability of biofilm formation among β-lactamase-producing uropathogenic Escherichia coli (UPEC) could facilitate the exchange of antibiotic-resistance genes, which resulted in widespread dissemination of antibacterial drug resistance. We investigated the prevalence of biofilm and β-lactamase producing UPECs among patients with urinary tract infection (UTI) in two cities with different demographics and climates in Iran. A total of 265 E. coli was isolated from patients with UTIs from two referral hospitals (n = 191) and two outpatient clinics (n = 74) in Isfahan and Zahedan, Iran. Production of curli and cellulose, and, biofilm formation was investigated using Congo red agar and microtiter plate methods, respectively. Biofilm producing (BFP) isolates (n = 107) were further characterized using rep-PCR, antimicrobial susceptibility testing and extended-spectrum β-lactamase (ESBL)/AmpC phenotypic production. Isolates were also screened for the presence of carbapenemase, ESBL and AmpC genes using multiplex PCR.   High diversity was found among BFP strains in both cities, with 58% strains producing ESBL and 21% producing AmpC. ESBL (98%), AmpC (50%) and carbapenemase genes (40%) were identified in BFP strains with ESBL-positive phenotype, respectively. The prevalence of BFP strains, antibiotic resistance and β-lactamase genes in Zahedan, a low socioeconomic city with a warm climate, was significantly higher than that of Isfahan. High prevalence of biofilm and β-lactamase producing UPEC strains among strains from Zahedan suggests that socioeconomic status and environmental factors might have a role in pathogenicity of the strains.

Prevalence of extended-spectrum β-lactamases, AmpC, and carbapenemases in Proteus mirabilis clinical isolates

Background

Proteus mirabilis is an opportunistic pathogen, causing a variety of community-acquired and nosocomial illnesses. It poses a potential threat to patients via the production of β-lactamases, which decrease the efficacy of antimicrobial treatment and impair the management of its pathogenicity. Hence, this study was established to determine the prevalence of extended-spectrum β-lactamases (ESBLs), AmpC, and carbapenemases of P. mirabilis isolated from various clinical specimens.

Results

Proteus mirabilis was identified in 20.7% (58/280) of specimens. ESBL producers were present at a rate of 51.7% (30/58). All AmpC-positive isolates (n = 20) produced ESBLs as well, so 66.7% of ESBL-producing isolates coproduced AmpC enzymes. The modified Hodge test confirmed carbapenemase production in six out of seven imipenem nonsusceptible isolates. Of these, only two (5.7%) isolates were also ESBL-and AmpC-positive. Antibiotic resistance reached the highest level for cotrimoxazole (62.1%, n = 36/58 isolates) and the lowest for imipenem (12.1%, n = 7/58 isolates). The levels of multidrug-resistant (MDR) was 41.4% among the tested isolates. The bla_SHV (83.3%), bla_AmpC (80%), and bla_VIM-1 (50%) were the most detected genes in phenotypically confirmed ESBL-, AmpC-, and carbapenemase-producing isolates, respectively. Besides, more than a half of the tested P. mirabilis strains (53%) coproduced ESBLs and AmpC. Moreover, two isolates coproduced ESBLs and AmpC together with carbapenemases. Furthermore, dendrogram analysis showed great genetic divergence based on the 21 different enterobacterial repetitive intergenic consensus (ERIC) patterns (P1–P21) through the 34 β-lactamase producers. ERIC analysis distinguished clonal similarities between isolates 21 and 22 in P2 and 9 and 10 in P4, which were isolated from the same clinical source and possessed similar patterns of β-lactamase-encoding genes.

Conclusion

Hence, there is an urgent need to monitor hospitalized patients and improve healthcare in order to reduce the incidence of infection and outbreaks of infection with antibiotic-resistant Proteus.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02662-3.

Gastrointestinal colonization of Extended-Spectrum Beta lactamase producing bacteria among children below five years of age hospitalized with fever in Dar es Salaam, Tanzania

BACKGROUND

Gastrointestinal colonization of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) is of concern because prior colonization increases risk for subsequent infections. To date, the link between ESBL-PE fecal carriage and the risk of subsequent ESBL-PE infection has not been well established, and information on carriage of such pathogens among children with invasive infections such as blood stream infections (BSI) remains to be explored worldwide.

METHODS

This cross-sectional study was conducted among childrenunder the age of 5 years admitted for febrile illness in Dar es Salaam, Tanzania, between March 2017 and July 2018. We used rectal swabs to screen for ESBL-PE using selective media, ChromID® ESBL. Bacterial isolates were identified by MALDI-TOF.Blood cultures were drawn from all children. Antimicrobial susceptibility testingwas done using disk diffusion method. ESBL alleles were identified by Real-Time PCR and sequencing.

RESULTS

The overall prevalence of ESBL-PE carriage was 56% (112/200) and washighestamong children 4-6 months old (17/21, 81%) (p =0.05). Children with BSI had high ESBL-PE carriage (78.4%) compared to those without BSI (53.1%)(p=0.02; AOR 3.4, 95% CI1.20-9.58).The most common isolate was E.coli (64/112, 45%). Sixteen pairs of ESBL-PEisolates(from the gut and from blood)had similar antimicrobial susceptibility profile. We detectedbla_CTX-M gene in 97% of all phenotypically detected ESBL-PE; among those,bla_CTX-M-15 was dominant (99%).

CONCLUSIONS

We report a high prevalence of ESBL-PEfecal carriage among children with BSI in Tanzania. Colonization of ESBL-PEwasa risk factor for ESBL-BSI.

Antibiotic-resistance genes in E. coli strains in GCC countries: A meta-analysis

Background:

Antimicrobial resistance (AMR) in Escherichia coli is an alarming issue worldwide, including in the Gulf Cooperation Council (GCC) countries, yet the prevailing gene patterns have not recently been reviewed. This study was conducted to determine and report on the dominant E. coli antimicrobial resistant gene patterns in GCC countries.

Method:

A scoping review identified the predominant AMR genes in GCC countries: CTX M, TEM, SHV, NDM, OXA, and VIM genes. For the systematic review, two authors independently searched Scopus, PubMed, Google Scholar, Science Direct, and Web of Science for interventional, clinical, or observational studies on the chosen AMR-conferring genes in E. coli published from GCC countries between January 2013 and June 2019, when the last search was carried out. The search strategy followed the PRISMA guidelines. The risk of bias was assessed using a 6-item standardized checklist. Random-effects modeling was used for all analyses.

Results:

A total 32 studies were included in the final synthesis of evidence. Overall, CTX-M (53.8%) was the most prevalent gene in the region followed TEM (40.6%), NDM-1 (28.4%), OXA (24.3%), VIM (8.5%), and SHV (7.8%). Most included studies were from Saudi Arabia: CTX-M was again most common with a prevalence of 46.8% from 5442 isolates.

Conclusion:

The risk of bias analysis showed a mean quality score of 4.25 ± 0.75, indicating high-quality in studies included in this meta-analysis. This review found that CTX-M gene is the most common AMR-conferring gene in E. coli strains from most GCC countries.

Genetic relatedness in extended-spectrum beta-lactamase-producing Escherichia coli from clinical isolates using enterobacterial repetitive intergenic consensus polymerase chain reaction

OBJECTIVES

The aim of this study is to determine the genetic relatedness of extended-spectrum beta-lactamases (ESBL)-producing Escherichia coli using the enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) technique.

METHODS

Suspected Gram-negative bacteria with their identities from the clinical samples were confirmed using Microgen GN-A-ID Kit. The double-disc synergy test was used to confirm for ESBL-producing E. coli. The susceptibility of the organisms was tested against eleven antimicrobial agents. A singleplex PCR assay was carried out targeting TEM, SHV, CTX-M, and OXA. ERIC-PCR performed, and band patterns obtained were visually evaluated. A dendrogram of the ERIC-PCR fingerprint pattern was done with the aid of DendroUPGMA using the cluster method.

RESULTS

Of the 576 clinical samples collected, 23 isolates were confirmed E. coli, and all (100%) are ESBL producers. The highest antibiotic resistance rate was recorded in cefixime (95.6%), and the least was amikacin (17.4%). The predominant ESBL gene is blaTEM genes (95.6%). Gel analysis of ERIC-PCR revealed 1-6 bands. The profiles of the ERIC-PCR differentiated the 23 E. coli isolates into four ERIC cluster types.

CONCLUSION

More than 80% of the isolates are sensitive to amikacin, with greater than 95% harboring blaTEM genes. Overall, ERIC obtained from the clinical specimens indicated some evidence in the genetic relatedness of the ESBL genes among E. coli isolates.

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.

Phenotypic and genotypic detection of extended spectrum β-lactamases among Escherichia coli and Klebsiella pneumoniae isolates from type 2 diabetic patients with urinary tract infections

Background

T2DM patients are more likely to have UTIs caused by resistant organisms such as ESBLs producing bacteria. Challenging reliable identification and prompt characterization of in-vitro susceptibilities of these bacteria are the first steps of deciding the appropriate antimicrobial therapy for UTIs caused by them.

Objectives

To isolate and identify E. coli and K. pneumoniae from urine of T2DM patients with UTIs, to determine antibiotic resistance pattern among isolates, and to identify ESBLs production phenotypically and genotypically.

Material and method

All samples were cultured on Cystine-Lactose-Electrolyte-Deficient Agar medium (CLED) by using calibrated loop. Growth of 100 colonies or more, i.e. 105 colony forming units (CFU)/mL urine was considered as significant bacteriuria. Isolation and identification were done according to standard method. All isolates were tested for antibiotic susceptibility testing by the disc diffusion method according to CLSI guidelines. Phenotypic detection of ESBLs was done by double-disk synergy test. Genotypic detection of blaTEM, blaSHV and blaCTX-M genes by using PCR.

Results

Results of this study showed that E. coli and K. pneumoniae were the dominant bacterial isolates, they constituted 103 (91.2%) out of 113 urine isolates. E. coli (58. 4%) K. pneumoniae (32.7%), Enterococcus spp. (4.4%), Proteus spp. (2.7%) and Pseudomonas spp. (1.8%). About 25 (24.3%) out of 103 E. coli and K. pneumoniae isolates were ESBLs positive by DDST, and 22 (88.0%) out of them had ESBLs encoding genes by conventional PCR. The most common gene detected was blaTEM (59.1%), followed by blaSHV (27.3%). CTX-M had not been detected in any of testes isolates.

Conclusion

blaTEM and blaSHV genes were detected in 22 out of 25 ESBLs producing E. coli and K. pneumoniae isolates phenotypically detected by DDST. blaTEM was found to be the predominant gene (59.1%), while blaCTX-Mene was not detected in any of tested isolates.

Rodent-Related Zoonotic Pathogens at the Human-Animal-Environment Interface in Qatar: A Systematic Review and Meta-Analysis

Rodents are one of the most diversified terrestrial mammals, and they perform several beneficial activities in nature. These animals are also important as carriers of many pathogens with public health importance. The current systematic review was conducted to formulate a true depiction of rodent-related zoonoses in Qatar. Following systematic searches on PubMed, Scopus, Science Direct, and Web of Science and a screening process, a total of 94 published articles were selected and studied. The studied articles reported 23 rodent-related zoonotic pathogens that include nine bacterial, eleven parasitic, and three viral pathogens, from which the frequently reported pathogens were Mycobacterium tuberculosis (32 reports), Escherichia coli (23), and Salmonella spp. (16). The possible pathway of entry of the rodent-borne pathogens can be the land port, seaports, and airport of Qatar through carrier humans and animals, contaminated food, and agricultural products. The pathogens can be conserved internally by rodents, pets, and livestock; by agricultural production systems; and by food marketing chains. The overall estimated pooled prevalence of the pathogens among the human population was 4.27% (95%CI: 4.03–4.51%; p < 0.001) with significant heterogeneity (I² = 99.50%). The top three highest prevalent pathogens were M.tuberculosis (30.90%; 22.75–39.04%; p < 0.001; I² = 99.70%) followed by Toxoplasma gondii (21.93%; 6.23–37.61%; p < 0.001; I² = 99.30%) and hepatitis E virus (18.29%; 11.72–24.86%; p < 0.001; I² = 96.70%). However, there is a knowledge gap about the listed pathogens regarding the occurrence, transmission pathways, and rodent role in transmission dynamics at the human–animal–environment interface in Qatar. Further studies are required to explore the role of rodents in spreading zoonotic pathogens through the One Health framework, consisting of zoologists, ecologists, microbiologists, entomologists, veterinarians, and public health experts in this country.

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.

Comprehensive study of antimicrobial susceptibility pattern and extended spectrum beta-lactamase (ESBL) prevalence in bacteria isolated from urine samples

Nowadays, increasing extended-spectrum β-lactamase (ESBL)-producing bacteria have become a global concern because of inducing resistance toward most of the antimicrobial classes and making the treatment difficult. In order to achieve an appropriate treatment option, identification of the prevalent species which generate ESBL as well as their antibiotic susceptibility pattern is essential worldwide. Hence, this study aimed to investigate the prevalence of ESBL-producing bacteria and assess their drug susceptibility in Fardis Town, Iran. A total of 21,604 urine samples collected from patients suspected to have urinary tract infection (UTI) were processed in the current study. The antimicrobial susceptibility of the isolates was tested by the disk diffusion method. The ESBL producing bacteria were determined by Double Disc Synergy Test (DDST) procedure. Bacterial growth was detected in 1408 (6.52%) cases. The most common bacterial strains causing UTI were found E. coli (72.16%), followed by K. pneumoniae (10.3%) and S. agalactiae (5.7%). Overall, 398 (28.26%) were ESBL producer. The highest ESBL production was observed in E. coli, followed by Klebsiella species. ESBL producers revealed a higher level of antibiotic resistance compared with non-ESBLs. In conclusion, ESBL production in uropathogens was relatively high. Carbapenems and Aminoglycosides were confirmed as the most effective treatment options for these bacteria.

Comprehensive study of antimicrobial susceptibility pattern and extended spectrum beta-lactamase (ESBL) prevalence in bacteria isolated from urine samples

Nowadays, increasing extended-spectrum β-lactamase (ESBL)-producing bacteria have become a global concern because of inducing resistance toward most of the antimicrobial classes and making the treatment difficult. In order to achieve an appropriate treatment option, identification of the prevalent species which generate ESBL as well as their antibiotic susceptibility pattern is essential worldwide. Hence, this study aimed to investigate the prevalence of ESBL-producing bacteria and assess their drug susceptibility in Fardis Town, Iran. A total of 21,604 urine samples collected from patients suspected to have urinary tract infection (UTI) were processed in the current study. The antimicrobial susceptibility of the isolates was tested by the disk diffusion method. The ESBL producing bacteria were determined by Double Disc Synergy Test (DDST) procedure. Bacterial growth was detected in 1408 (6.52%) cases. The most common bacterial strains causing UTI were found E. coli (72.16%), followed by K. pneumoniae (10.3%) and S. agalactiae (5.7%). Overall, 398 (28.26%) were ESBL producer. The highest ESBL production was observed in E. coli, followed by Klebsiella species. ESBL producers revealed a higher level of antibiotic resistance compared with non-ESBLs. In conclusion, ESBL production in uropathogens was relatively high. Carbapenems and Aminoglycosides were confirmed as the most effective treatment options for these bacteria.

Prevalence and molecular characteristics of ESBL and AmpC β -lactamase producing Enterobacteriaceae strains isolated from UTIs in Egypt

BACKGROUND

Infections caused by Enterobacteriaceae are mainly treated with the β-lactam antibiotics, nevertheless, the emergence of species with plasmid-borne β-lactamases has decreased the efficacy of these antibiotics. Therefore, continuing studies on the resistance pattern of different regions is important for assessment of proper antimicrobial therapy protocols. The study aimed to characterize extended-spectrum β-lactamase (ESBL) and AmpC β -lactamase (AmpC) producing Enterobacteriaceae isolated from community-acquired UTIs in Egypt.

METHODS

Out of 705 urine samples, 440 Enterobacteriaceae isolates were investigated to detect ESBL and AmpC β -lactamases producers by phenotypic and molecular methods.

RESULTS

Out of 440 Enterobacteriaceae isolates, 311 were identified as ESBL producers by phenotypic testing. ESBL genes were detected in 308 isolates. BlaCTX-M-type was the most prevalent 254 (81.6%), out of them blaCTXM-15 was the commonest (152, 48.8%) followed by blaCTX-M-1 (140, 45%), blaCTX-M-8 (72, 23.1%) and lastly blaCTX-M-2 (4, 1.3%). blaTEM gene also was detected in a high rate (189, 60.7%). Two hundred and thirty-five (75.5%) of ESBL producers harbored blaCTX-M in combination with blaTEM and/or blaSHV genes. Multiple drug resistance in the ESBL-producers was significantly (P < 0.05) higher than in non-ESBL producers. Imipenem was the most effective drug against ESBL producers. Among 35 cefoxitin resistant isolates, 18 (51.4%) identified as carrying AmpC genes by multiplex PCR. Within AmpC β -lactamase genes, DHA gene was the predominant gene (15, 42.3%). CIT and MOX genes were also present, but in a low rate (5, 14.2% and 4, 11.4%) respectively. Co-existence of multiple AmpC genes was detected exclusively in K. pneumoniae isolates. E. coli isolates harbored DHA gene only. However, FOX gene was not detected in the study isolates. Seventeen of isolates carrying AmpC genes were also positive for ESBL genes.

CONCLUSION

The study shows that the prevalence of ESBL producing Enterobacteriaceae spread in south Egypt is alarming, however AmpC β -lactamase production is not so high.

Prevalence of Antibiotic-Resistant Escherichia coli Isolates from Local and Imported Retail Chicken Carcasses

ABSTRACT

The spread of antibiotic resistance among bacterial strains has been associated with consumption of food contaminated with both pathogenic and nonpathogenic bacteria. The objective of this study was to determine the prevalence of antibiotic resistant Escherichia coli isolates in local and imported retail raw chicken meat in Qatar. A total of 270 locally produced (chilled) and imported (chilled or frozen) whole chicken carcasses were obtained from three Hypermarket stores in Qatar. The 216 E. coli isolates recovered from the chicken samples were subjected to antibiotic susceptibility testing with the disk diffusion method. Extended-spectrum β-lactamase (ESBL) production was evaluated with the double disk synergy test. Isolates harboring colistin resistance were identified with a multiplex PCR assay and DNA sequencing. Nearly 89% (192) of the 216 isolates were resistant to at least one of the 18 antibiotics tested. Isolates from local and imported chicken carcasses had relatively higher resistance to sulfamethoxazole (62% of isolates), tetracycline (59.7%), ampicillin and trimethoprim (52.3% each), ciprofloxacin (47.7%), cephalothin (45.4%), and colistin (31.9%). Less resistance was found to amoxicillin-clavulanic acid (6%), ceftriaxone (5.1%), nitrofurantoin (4.2%), piperacillin-tazobactam (4.2%), cefepime (2.3%), meropenem (1.4%), ertapenem (0.9%), and amikacin (0.9%). Nine isolates (4.2%) were ESBL producers, and 137 (63.4%) were multidrug resistant. The percentages of multidrug-resistant, ESBL-producing, and colistin resistant isolates were significantly higher among isolates from local chilled than from imported chilled and frozen chicken samples. Our findings indicate the high prevalence of antibiotic-resistant E. coli in chicken meat sold at retail in Qatar.

HIGHLIGHTS

Molecular Characterization of Extended-Spectrum β-Lactamase-Producing Escherichia coli and Klebsiella pneumoniae Among the Pediatric Population in Qatar

INTRODUCTION

Although extended-spectrum β-lactamase (ESBL)-producing Enterobacterales are a public health problem in the Arabian Peninsula, data on the molecular characteristic of their antimicrobial resistance determinants in children is limited.

AIM

To determine the molecular characteristics of ESBL-producing Escherichia coli and Klebsiella pneumoniae in the pediatric population of Qatar.

METHODS

Whole-genome sequencing was performed on ESBL-producing E. coli and K. pneumoniae isolates recovered from screening and clinical specimens from pediatric patients at Sidra Medicine in Doha from January to December 2018.

RESULTS

A total of 327 ESBL producers were sequenced: 254 E. coli and 73 K. pneumoniae. Non-susceptibility rates to non-β-lactam antibiotics for both species were 18.1 and 30.1% for gentamicin, 0.8 and 4.1% for amikacin, 41.3 and 41.1% for ciprofloxacin, and 65.8 and 76.1% for cotrimoxazole. The most common sequence types (STs) were ST131 (16.9%), ST38 and ST10 (8.2% each) in E. coli and ST307 (9.7%), and ST45 and ST268 (6.9% each) in K. pneumoniae. CTX-M type ESBLs were found in all but one isolate, with CTX-M-15 accounting for 87.8%. Among other β-lactamases, TEM-1B and OXA-1 were coproduced in 41 and 19.6% of isolates. The most common plasmid-mediated quinolone resistance genes cocarried were qnr A/B/E/S (45.3%). Ninety percent of gentamicin non-susceptible isolates harbored genes encoding AAC(3) enzymes, mainly aac(3)-IIa. Only two of 57 isolates harboring aac(6')-Ib-cr were non-susceptible to amikacin. Chromosomal mutations in genes encoding DNA gyrase and topoisomerase IV enzymes were detected in 96.2% fluoroquinolone-non-susceptible E. coli and 26.7% fluoroquinolone-non-susceptible K. pneumoniae.

CONCLUSION

Our data show that CTX-M enzymes are largely the most prevalent ESBLs in children in Qatar with a predominance of CTX-M-15. Carbapenem-sparing options to treat ESBL infections are limited, given the frequent coproduction of OXA-1 and TEM-1B enzymes and coresistance to antibiotic classes other than β-lactams.

Retrospective Analysis on Antimicrobial Resistance Trends and Prevalence of β-lactamases in Escherichia coli and ESKAPE Pathogens Isolated from Arabian Patients during 2000-2020

The production of diverse and extended spectrum β-lactamases among Escherichia coli and ESKAPE pathogens is a growing threat to clinicians and public health. We aim to provide a comprehensive analysis of evolving trends of antimicrobial resistance and β-lactamases among E. coli and ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acine to bacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) in the Arabian region. A systematic review was conducted in Medline PubMed on papers published between January 2000 and February 2020 on countries in the Arab region showing different antibiotic resistance among E. coli and ESKAPE pathogens. A total of n = 119,144 clinical isolates were evaluated for antimicrobial resistance in 19 Arab countries. Among these clinical isolates, 74,039 belonged to E. coli and ESKAPE pathogen. Distribution of antibiotic resistance among E. coli and ESKAPE pathogens indicated that E. coli (n = 32,038) was the predominant pathogen followed by K. pneumoniae (n = 17,128), P. aeruginosa (n = 11,074), methicillin-resistant S. aureus (MRSA, n = 4370), A. baumannii (n = 3485) and Enterobacter spp. (n = 1574). There were no reports demonstrating Enterococcus faecium producing β-lactamase. Analyses revealed 19 out of 22 countries reported occurrence of ESBL (Extended-Spectrum β-Lactamase) producing E. coli and ESKAPE pathogens. The present study showed significantly increased resistance rates to various antimicrobial agents over the last 20 years; for instance, cephalosporin resistance increased from 37 to 89.5%, fluoroquinolones from 46.8 to 70.3%, aminoglycosides from 40.2 to 64.4%, mono-bactams from 30.6 to 73.6% and carbapenems from 30.5 to 64.4%. An average of 36.9% of the total isolates were reported to have ESBL phenotype during 2000 to 2020. Molecular analyses showed that among ESBLs and Class A and Class D β-lactamases, bla_CTX-M and bla_OXA have higher prevalence rates of 57% and 52.7%, respectively. Among Class B β-lactamases, few incidences of bla_VIM 27.7% and bla_NDM 26.3% were encountered in the Arab region. Conclusion: This review highlights a significant increase in resistance to various classes of antibiotics, including cephalosporins, β-lactam and β-lactamase inhibitor combinations, carbapenems, aminoglycosides and quinolones among E. coli and ESKAPE pathogens in the Arab region.

A systematic review on the prevalence of extended-spectrum beta lactamase-producing Gram-negative bacteria in Nigeria

OBJECTIVE

There are numerous reported cases of extended-spectrum beta-lactamases (ESBLs) producing Enterobacteriaceae in Nigeria. Yet, there are regions in Nigeria where cases of ESBL were under-reported. The review aims to assess the prevalence of ESBL-producing Gram-negative bacteria in Nigeria and the genes involved.

METHODS

An extensive literature search was carried out through an electronic database including PubMed, Scopus, Google Scholar and African Journals Online (AJOL). Articles published between January 2004 and November 2019 were included in the study. The titles and abstracts of the retrieved articles were reviewed, and then the full texts of the selected articles were reviewed. Articles were divided according to geopolitical zones.

RESULTS

Among the 217 articles identified, 60 studies (10 from north-central, 4 from northeast, 7 from the northwest, 17 from the southeast, 10 from south-south, and 12 from southwest Nigeria) were included. The highest prevalence recorded was 82.3%, while the lowest was 7.5%. The genes TEM, SHV, and CTX-M were the predominant variant commonly found. The most frequently used phenotypic detection method is the double disc synergy test (DDST).

CONCLUSION

ESBL-producing Gram-negative bacteria in hospital and community settings in Nigeria were commonly found. The prevalence of ESBL is very high, with one of the geopolitical zones under-reported. Future research should be conducted in these zones where there are scant studies, and a holistic approach involving the clinicians, researchers, laboratory scientists, and patients will go a long way in reducing the dissemination of this resistance mechanism.

Antibiotic resistance and virulence patterns of pathogenic Escherichia coli strains associated with acute gastroenteritis among children in Qatar

Background

The treatment of Enterobacteriaceae family including diarrheagenic E. coli (DEC) has been increasingly complicated due to the emergence of resistant strains. Here we report on the phenotypic resistance profiles and ESBL genotype and virulence profiles of Enteroaggregative E. coli (EAEC) and Enteropathogenic E. coli (EPEC) isolated from children hospitalized with acute gastroenteritis in Qatar (AGE).

Results

E. coli were isolated and characterized from 76 diarrheagenic stool positive samples, collected from hospitalized children less than 10 years old. Isolates were tested for antibiotic susceptibility against eighteen clinically relevant antibiotics using E-test method. Conventional PCR was performed to detect genes encoding ESBL and virulence factors. Chi-square test was performed to compare the individual antibiotic resistance between EPEC and EAEC.

A significant percentage (73.7%) of isolates were resistant to at least one antibiotic. Overall, high resistance (70%) was reported to the first-line antibiotics such as ampicillin, tetracycline (46.4%), and sulfamethoxazole-trimethoprim (42.9%). Further, 39.5% of the isolates were multidrug resistant (MDR), with 22.4% being ESBL producers. On the other hand, all isolates were susceptible to carbapenem, fosfomycin, amikacin and colistin. The incidences of resistance to the 18 antibiotics between EPEC and EAEC were not significantly different by Pearson chi -square test (P > 0.05). Genetic analysis revealed that 88.23% of ESBL production was bla_CTX-M-G1 (bla_CTX-M-15, bla_CTX-M-3) - encoded. Several different combinations of virulence markers were observed, however, there was no specific trend among the isolates apart from absence of the bundle-forming pilus (bfpA) gene, which encodes the type IV fimbriae in EPEC adherence factor (EAF) plasmid (pEAF), among all EPEC (atypical). 15% of the EAEC strains were positive for a combination of astA, aap & capU, while 10% were positive for three different combinations. The aap, aatA, capU and aggR virulence genes showed the highest frequency of 65, 60, 55 and 55% respectively. Others genes, east, astA, and aai, showed frequencies of 35, 30 and 20% respectively.

Conclusions

Atypical EPEC and EAEC were the primary etiological agents of diarrhea in children among DEC pathotypes. Our results indicated high rate of antimicrobial resistance pattern of DEC strains, which necessities the development of regulatory programs and reporting systems of antimicrobial resistance in DEC and other AGE-associated bacteria to insure effective control of diarrheal diseases. Results from this study demand a further research on identifying the phenotypic and genotypic profiles of more DEC pathotypes in various clinical samples.

Phenotypic and Molecular Characterization of β-Lactamases among Enterobacterial Uropathogens in Southeastern Nigeria

Little is known about the molecular basis of antibiotic resistance among uropathogens in Southeast Nigeria. The aim of the study was to characterize enterobacterial uropathogens with respect to drug resistance. One hundred (100) enterobacterial uropathogens were studied. Their antibiotic susceptibility patterns were evaluated using disk diffusion, screened, and confirmed phenotypically for the presence of β-lactamases: ESBL, AmpC, carbapenemase, and MBLs. Screen positives were further tested for various β-lactamase genes by PCR. Our isolates showed variable resistance to most drugs tested. Out of the 58 ESBL screen positive E. coli, 35 were confirmed positive with PCR. The predominant ESBL gene was bla_TEM while bla_SPM was the most prevalent among MBL genes. Forty-six percentage of the screen positive Salmonella isolates coharbored bla_{TEM + SHV} genes. Nine of the 10 ESBL screen positive K. pneumoniae were phenotypically and PCR positive. Three isolates of K. pneumoniae were positive for MBL genes. All the 10 C. freundii were positive for ESBL genes. The study showed high prevalence of drug-resistant genes among the enterobacterial uropathogens. Majority of the uropathogens harbored >1 antibiotic-resistant gene, and the most predominant gene was ESBL (bla_TEM) followed by the MBL (SPM) gene.

Extended-Spectrum β-Lactamases among Enterobacteriaceae Isolated from Urinary Tract Infections in Gaza Strip, Palestine

Background

Extended-spectrum β-lactamase-producing organisms causing urinary tract infections are increasing in incidence and pose a major impendence to health-care facility, having limited therapeutic options. This study aimed to assess the prevalence of ESBLs in Enterobacteriaceae isolates causing urinary tract infections in Gaza strip, Palestine, and to characterize β-lactamase types and associated resistance genes.

Methods

Eighty-five Enterobacteriaceae isolates were recovered from urinary tract infections within three months in Gaza Strip hospitals. The characterization of β-lactamase genes and the genetic environments of CTX-M, the identification of associated resistance genes, and the presence and characterization of integrons were tested by PCR and sequencing.

Results

The occurrence rate of ESBL among tested isolates was 30 (35.3%), and among ESBL-positive isolates, bla_CTX-M was the highest followed by bla_TEM. ESBL-CTX-M-1 group was confirmed in 93.3%, and the remaining carried CTX-M-9 group. CTX-M-15, CTX-M-3, CTX-M-1, CTX-M-14, CTX-M-27, and CTX-M-37 enzymes were demonstrated among the isolates with the majority (73%) being CTX-M-15. ISEcp-1 was demonstrated in 27 (90%, high incidence) of ESBL isolates. Class 1 integrons have been detected in higher rates (53.3%) in ESBL-positive isolates in comparison with non-ESBL isolates (6, 33.3%). Cassettes of integron-1 contain (aadA1, aadA2, aadA5, dfrA5, dfrA7, dfrA12, and dfrA17) genes. The aac(6′)-Ib-cr gene was demonstrated in 36.7% of ESBL-positive isolates.

Conclusions

This study indicates that bla_CTX-M-15 was the most prevalent β-lactamase in this region. Our study demonstrates for the first time in Palestine the identification of bla_CTX-M-15 in P. rettgeri and S. liquefaciens, also bla_CTX-M-37 in E. cloacae. The coexpression of multiple β-lactamase genes with aac(6′)-Ib-cr and qnr in the presence of ISEcp-1 and integrons in individual strains will increase the dissemination of highly resistant strains. ESBL producers were more resistant than non-ESBLs producers for almost all tested antibiotics.

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.

"Enhanced acquisition of antibiotic-resistant intestinal E. coli during the first year of life assessed in a prospective cohort study"

Background

Increasing bacterial resistance to antibiotics is a serious problem worldwide. We sought to record the acquisition of antibiotic-resistant Escherichia coli (E. coli) in healthy infants in Northern Thailand and investigated potential determinants.

Methods

Stool samples from 142 infants after birth, at ages 2wk, 2mo, 4 to 6mo, and 1y, and parent stool samples were screened for E. coli resistance to tetracycline, ampicillin, co-trimoxazole, and cefazoline by culture, and isolates were further investigated for multiresistance by disc diffusion method. Pulsed-field gel electrophoresis was performed to identify persistent and transmitted strains. Genetic comparison of resistant and transmitted strains was done by multilocus sequence typing (MLST) and strains were further investigated for extra- and intra-intestinal virulence factors by multiplex PCR.

Results

Forty-seven (33%) neonatal meconium samples contained resistant E. coli. Prevalence increased continuously: After 1y, resistance proportion (tetracycline 80%, ampicillin 72%, co-trimoxazole 66%, cefazoline 35%) almost matched those in parents. In 8 infants (6%), identical E. coli strains were found in at least 3 sampling time points (suggesting persistence). Transmission of resistant E. coli from parents to child was observed in only 8 families. MLST showed high diversity. We could not identify any virulence genes or factors associated with persistence, or transmission of resistant E. coli. Full-term, vaginal birth and birth in rural hospital were identified as risk factors for early childhood colonization with resistant E. coli.

Conclusion

One third of healthy Thai neonates harboured antibiotic-resistant E. coli in meconium. The proportion of resistant E. coli increased during the first year of life almost reaching the value in adults. We hypothesize that enhancement of infection control measures and cautious use of antibiotics may help to control further increase of resistance.

Electronic supplementary material

The online version of this article (10.1186/s13756-019-0522-6) contains supplementary material, which is available to authorized users.