Rapid identification of carbapenemase genes in gram-negative bacteria with an oligonucleotide microarray-based assay

Carbapenemase producing Gram negative bacteria: Review of resistance and detection methods

Gram negative bacilli that are carbapenem resistant have emerged and are spreading worldwide. Infections caused by carbapenem resistant isolates posses a significant threat due to their high morbidity and mortality rates. Carbapenemases production by multi-drug resistant pathogens severely restricts treatment choices for illnesses caused by bacteria that are resistant to both carbapenems and majority of β-lactam antibiotics. Various phenotypic and genotypic methods for identification can distinguish between different classes of carbapenemase and identify pathogens that are resistant to carbapenems. The establishment of a quick, accurate and reliable test for identifying the clinical strains that produce the carbapenemase enzyme is essential for optimum diagnosis of microbial pathogens and management of the global rise in the prevalence of carbapenemase producing bacterial strains. The aim of this review was to summarize the mechanisms of carbapenem resistance and to provide an overview of different carbapenemase detection methods for carbapenem resistant Gram negative bacilli.

Occurrence, Phenotypic and Molecular Characteristics of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in Healthy Turkeys in Northern Egypt

Poultry is one of the most important reservoirs for zoonotic multidrug-resistant pathogens. The indiscriminate use of antimicrobials in poultry production is a leading factor for development and dissemination of antimicrobial resistance. This study aimed to describe the prevalence and antimicrobial resistance of E. coli isolated from healthy turkey flocks of different ages in Nile delta region, Egypt. In the current investigation, 250 cloacal swabs were collected from 12 turkey farms in five governorates in the northern Egypt. Collected samples were cultivated on Brilliance^TM ESBL agar media supplemented with cefotaxime (100 mg/L). The E. coli isolates were identified using MALDI-TOF-MS and confirmed by a conventional PCR assay targeting 16S rRNA-DNA. The phenotypic antibiogram against 14 antimicrobial agents was determined using the broth micro-dilution method. DNA-microarray-based assay was applied for genotyping and determination of both, virulence and resistance-associated gene markers. Multiplex real-time PCR was additionally applied for all isolates for detection of the actual most relevant Carbapenemase genes. The phenotypic identification of colistin resistance was carried out using E-test. A total of 26 E. coli isolates were recovered from the cloacal samples. All isolates were defined as multidrug-resistant. Interestingly, two different E. coli strains were isolated from one sample. Both strains had different phenotypic and genotypic profiles. All isolates were phenotypically susceptible to imipenem, while resistant to penicillin, rifampicin, streptomycin, and erythromycin. None of the examined carbapenem resistance genes was detected among isolates. At least one beta-lactamase gene was identified in most of isolates, where blaTEM was the most commonly identified determinant (80.8%), in addition to blaCTX-M9 (23.1%), blaSHV (19.2%) and blaOXA-10 (15.4%). Genes associated with chloramphenicol resistance were floR (65.4%) and cmlA1 (46.2%). Tetracycline- and quinolone-resistance-associated genes tetA and qnrS were detected in (57.7%) and (50.0%) of isolates, respectively. The aminoglycoside resistance associated genes aadA1 (65.4%), aadA2 (53.8%), aphA (50.0%), strA (69.2%), and strB (65.4%), were detected among isolates. Macrolide resistance associated genes mph and mrx were also detected in (53.8%) and (34.6%). Moreover, colistin resistance associated gene mcr-9 was identified in one isolate (3.8%). The class 1 integron integrase intI1 (84.6%), transposase for the transposon tnpISEcp1 (34.6%) and OqxB -integral membrane and component of RND-type multidrug efflux pump oqxB (7.7%) were identified among the isolates. The existing high incidence of ESBL/colistin-producing E. coli identified in healthy turkeys is a major concern that demands prompt control; otherwise, such strains and their resistance determinants could be transmitted to other bacteria and, eventually, to people via the food chain.

Uncovering antimicrobial resistance in three agricultural biogas plants using plant-based substrates

Antimicrobial resistance (AMR) is becoming an increasing global concern and the anaerobic digestion (AD) process represents a potential transmission route when digestates are used as fertilizing agents. AMR contaminants, e.g. antibiotic-resistant bacteria (ARB) and plasmid-mediated antibiotic resistance genes (ARGs) have been found in different substrates and AD systems, but not yet been investigated in plant-based substrates. AMR transfer from soils to vegetable microbiomes has been observed, and thus crop material potentially represents a so far neglected AMR load in agricultural AD processes, contributing to AMR spread. In order to test this hypothesis, this study examined the AMR situation throughout the process of three biogas plants using plant-based substrates only, or a mixture of plant-based and manure substrates. The evaluation included a combination of culture-independent and -dependent methods, i.e., identification of ARGs, plasmids, and pathogenic bacteria by DNA arrays, and phylogenetic classification of bacterial isolates and their phenotypic resistance pattern. To our knowledge, this is the first study on AMR in plant-based substrates and the corresponding biogas plant. The results showed that the bacterial community isolated from the investigated substrates and the AD processing facilities were mainly Gram-positive Bacillus spp. Apart from Pantoea agglomerans, no other Gram-negative species were found, either by bacteria culturing or by DNA typing array. In contrast, the presence of ARGs and plasmids clearly indicated the existence of Gram-negative pathogenic bacteria, in both substrate and AD process. Compared with substrates, digestates had lower levels of ARGs, plasmids, and culturable ARB. Thus, digestate could pose a lower risk of spreading AMR than substrates per se. In conclusion, plant-based substrates are associated with AMR, including culturable Gram-positive ARB and Gram-negative pathogenic bacteria-associated ARGs and plasmids. Thus, the AMR load from plant-based substrates should be taken into consideration in agricultural biogas processing.

Characterization of Enterococci- and ESBL-Producing Escherichia coli Isolated from Milk of Bovides with Mastitis in Egypt

This study aimed to investigate the prevalence and antimicrobial resistance of enterococci- and ESBL-producing E. coli isolated from milk of bovine mastitis cases in Egypt. Fifty milk samples of dairy animals were collected from localities in the Nile Delta region of Egypt. Isolates were identified using MALDI-TOF MS, and antibiotic susceptibility testing was performed by the broth microdilution method. PCR amplifications were carried out, targeting resistance-associated genes. Seventeen Enterococcus isolates and eight coliform isolates could be cultivated. Vancomycin resistance rate was high in Ent. faecalis. The VITEK 2 system confirmed all E. coli isolates as ESBL-producing. All Ent. faecalis isolates harbored erm(B), tetL and aac-aphD genes. The vanA gene was detected in Ent. faecalis isolate, vanB was found in other Enterococcus, while one isolate of E. casseliflavus exhibited the vanA gene. E. coli isolates exhibited high prevalence of erm(B) and tetL. E. coli isolates were analyzed by DNA microarray analysis. Four isolates were determined by O-serotyping as O8 (n = 1), O86 (n = 2) and O157 (n = 1). H-serotyping resulted in H11, H12, H21 (two isolates each) and one was of H16 type. Different virulence-associated genes were detected in E. coli isolates including lpfA, astA, celB, cmahemL, intI1 and intI2, and the iroN gene was identified by DNA microarray analysis.

Molecular characterisation of extended-spectrum ß-lactamase producing Escherichia coli in wild birds and cattle, Ibadan, Nigeria

Background

Antimicrobial resistance (AMR) is an increasing global health concern reducing options for therapy of infections and also for perioperative prophylaxis. Many Enterobacteriaceae cannot be treated anymore with third generation cephalosporins (3GC) due to the production of certain 3GC hydrolysing enzymes (extended spectrum beta-lactamases, ESBLs). The role of animals as carriers and vectors of multi-resistant bacteria in different geographical regions is poorly understood. Therefore, we investigated the occurrence and molecular characteristics of ESBL-producing Escherichia coli (E. coli) in wild birds and slaughtered cattle in Ibadan, Nigeria.

Cattle faecal samples (n = 250) and wild bird pooled faecal samples (cattle egrets, Bubulcus ibis, n = 28; white-faced whistling duck, Dendrocygna viduata, n = 24) were collected and cultured on cefotaxime-eosin methylene blue agar. Antimicrobial susceptibility was determined by agar diffusion assays and all 3GC resistant isolates were genotypically characterised for AMR genes, virulence associated genes (VAGs) and serotypes using DNA microarray-based assays.

Results

All 3GC resistant isolates were E. coli: cattle (n = 53), egrets (n = 87) and whistling duck (n = 4); cultured from 32/250 (12.8%), 26/28 (92.9%), 2/24(8.3%), cattle, egrets and whistling duck faecal samples, respectively. blaCTX-M gene family was prevalent; blaCTX-M15 (83.3%) predominated over blaCTX-M9 (11.8%). All were susceptible to carbapenems. The majority of isolates were resistant to at least one of the other tested antimicrobials; multidrug resistance was highest in the isolates recovered from egrets.

The isolates harboured diverse repositories of other AMR genes (including strB and sul2), integrons (predominantly class 1) and VAGs. The isolates recovered from egrets harboured more AMR genes; eight were unique to these isolates including tetG, gepA, and floR. The prevalent VAGs included hemL and iss; while 14 (including sepA) were unique to certain animal isolates. E. coli serotypes O9:H9, O9:H30 and O9:H4 predominated. An identical phenotypic microarray profile was detected in three isolates from egrets and cattle, indicative of a clonal relationship amongst these isolates.

Conclusion

Wild birds and cattle harbour diverse ESBL-producing E. coli populations with potential of inter-species dissemination and virulence. Recommended guidelines to balance public health and habitat conservation should be implemented with continuous surveillance.

Convergence of carbapenem resistance and hypervirulence in a highly-transmissible ST11 clone of K. pneumoniae: An epidemiological, genomic and functional study

Co-occurrence of hypervirulence and KPC-2 carbapenem resistant phenotypes in a highly-transmissible ST11 clone ofKlebsiella pneumoniae has elicited deep concerns from public health stand point. To address this puzzle, we conducted a large-scale epidemiological, clinical and genomic study of K. pneumonia ST11 clones with both hypervirulence and carbapenem resistance in two tertiary hospitals in Zhejiang province. Most of the patients (15/23) were diagnosed with exclusively carbapenem-resistant K. pneumoniae (CRKP) infections. Ten death cases were reported, some of which are due to the failure of antibiotic therapies. As a result, we identified one new rare sequence types (ST449) to KPC-2-producing CRKP, in addition to the dominant ST11. These clinical isolates of K. pneumoniae are multi-drug resistant and possess a number of virulence factors. Experimental infections of wax moth larvae revealed the presence of hypervirulence at varied level, suggesting the complexity in bacterial virulence factors. However, plasmid curing assays further suggested that the rmpA2-virulence plasmid is associated with, but not sufficient for neither phenotypic hypermucoviscosity nor virulence of K. pneumoniae. Intriguingly, all the rmpA2 genes were found to be inactive due to genetic deletion. In total, we reported 21 complete plasmid sequences comprising 13 rmpA2-positive virulence plasmids and 8 bla _KPC-2-harboring resistance plasmids. In addition to the prevalent pLVKP-like virulence plasmid variants (~178kb), we found an unexpected diversity among KPC-2-producing plasmids whose dominant form is IncFII-IncR type (~120kb), rather than the previously anticipated version of ~170kb. These findings provide an updated snapshot of convergence of hypervirulence and carbapenem resistance in ST11 K. pneumoniae.

The prevalence of ampicillin-resistant opportunistic pathogenic bacteria undergoing selective stress of heavy metal pollutants in the Xiangjiang River, China

The emergence of clinically relevant β-lactam-resistant bacteria poses a serious threat to human health and presents a major challenge for medical treatment. How opportunistic pathogenic bacteria acquire antibiotic resistance and the prevalence of antibiotic-resistant opportunistic pathogenic bacteria in the environment are still unclear. In this study, we further confirmed that the selective pressure of heavy metals contributes to the increase in ampicillin-resistant opportunistic pathogens in the Xiangjiang River. Four ampicillin-resistant opportunistic pathogenic bacteria (Pseudomonas monteilii, Aeromonas hydrophila, Acinetobacter baumannii, and Staphylococcus epidermidis) were isolated on Luria-Bertani (LB) agar plates and identified by 16S rRNA sequencing. The abundance of these opportunistic pathogenic bacteria significantly increased in the sites downstream of the Xiangjiang River that were heavily influenced by metal mining activities. A microcosm experiment showed that the abundance of β-lactam resistance genes carried by opportunistic pathogenic bacteria in the heavy metal (Cu²⁺ and Zn²⁺) treatment group was 2-10 times higher than that in the control. Moreover, heavy metals (Cu²⁺ and Zn²⁺) significantly increased the horizontal transfer of plasmids in pathogenic bacteria. Of particular interest is that heavy metals facilitated the horizontal transfer of conjugative plasmids, which may lead to the prevalence of multidrug-resistant pathogenic bacteria in the Xiangjiang River.

High-throughput roll-to-roll production of polymer biochips for multiplexed DNA detection in point-of-care diagnostics

Roll-to-roll UV nanoimprint lithography has superior advantages for high-throughput manufacturing of micro- or nano-structures on flexible polymer foils with various geometries and configurations. Our pilot line provides large-scale structure imprinting for cost-effective polymer biochips (4500 biochips/hour), enabling rapid and multiplexed detections. A complete high-volume process chain of the technology for producing structures like μ-sized, triangular optical out-couplers or capillary channels (width: from 1 μm to 2 mm, height: from 200 nm up to 100 μm) to obtain biochips (width: 25 mm, length: 75 mm, height: 100 μm to 1.5 mm) was described. The imprinting process was performed with custom-developed resins on polymer foils with resin thicknesses ranging between 125-190 μm. The produced chips were tested in a commercial point-of-care diagnostic system for multiplexed DNA analysis of methicillin resistant Staphylococcus aureus (e.g., mecA, mecC gene detections). Specific target DNA capturing was based on hybridisation between surface bound DNA probes and biotinylated targets from the sample. The immobilised biotinylated targets subsequently bind streptavidin-horseradish peroxidase conjugates, which in turn generate light upon incubation with a chemiluminescent substrate. To enhance the light out-coupling thus to improve the system performance, optical structures were integrated into the design. The limits-of-detection of mecA (25 bp) for chips with and without structures were calculated as 0.06 and 0.07 μM, respectively. Further, foil-based chips with fluidic channels were DNA functionalised in our roll-to-roll micro-array spotter following the imprinting. This straightforward approach of sequential imprinting and multiplexed DNA functionalisation on a single foil was also realised for the first time. The corresponding foil-based chips were able to detect mecA gene DNA sequences down to a 0.25 μM concentration.

Broad-Spectrum Cephalosporin-Resistant and/or Fluoroquinolone-Resistant Enterobacterales Associated with Canine and Feline Urogenital Infections

The aim of the present study was to characterize Enterobacterales resistant to 3rd and 4th generation cephalosporins, carbapenems and/or fluoroquinolones, isolated from dogs and cats with urogenital infections. In total, 36 strains (Escherichia coli (n = 28), Klebsiella pneumoniae (n = 3), Serratia marcescens, Raoultella ornithinolytica, Proteus mirabilis, Citrobacter portucalensis and Enterobacter cloacae (each n = 1)) were included in the present study, 28 from Austria and 8 from Serbia. Isolates were characterized by a polyphasic approach including susceptibility pheno- and genotyping and microarray-based assays. Escherichia (E.) coli isolates were additionally characterized by two-locus (fumC and fimH) sequence phylotyping and multi-locus sequence typing (MLST) of selected isolates. MLST of carbapenem-resistant Enterobacter cloacae isolates was also performed. Among E. coli, the most dominant phylogenetic group was B1 (27.8%), followed by C, (16.6%), A and Clade II (5.5% each), B2 and F (2.77% each). The most predominant β-lactam resistance genes were blaTEM (70%) and blaCTX-M (38.8%), blaCMY (25%). blaNDM was detected in one carbapenem-resistant Enterobacter cloacae ST114. The most common ST among selected E. coli was 744 (10.7% isolates). The pandemic clones ST131 and ST648 carrying CTX-M-15 were also detected. Remaining STs belonged to 469, 1287, 1463 and 1642. E. coli clonotyping revealed 20 CH types. Based on the presence of certain virulence genes, three isolates were categorized as ExPEC/UPEC. The most prevalent virulence factors were fimH detected in 61%, iucD and iss both in 55%, iroN in 27.8%, papC in 13.8% and sat in 8.3% isolates.

Evaluation of the MBT STAR-Carba Assay for the Detection of Carbapenemase Production in Enterobacteriaceae and Hafniaceae with a Large Collection of Routine Isolates from Plate Cultures and Patient-Derived Positive Blood Cultures

The spread of carbapenemase-producing Enterobacterales is a major public health concern worldwide, and methods for their prompt and reliable detection are highly demanded for therapeutic and hygiene control purposes. In this study, we evaluate the MBT STAR^®-Carba assay (Bruker Daltonik) to detect the carbapenemase production in clinical and surveillance isolates from plate cultures and directly from patient-derived positive blood cultures bottles. Overall, n = 1,307 samples were analyzed (n = 900 plate cultures, and n = 407 positive blood cultures, using the bacterial pellet obtained with the Sepsityper^® Kit; Bruker Daltonik), including n = 793 carbapenemase producers (n = 579 Klebsiella pneumoniae carbapenemase, n = 161 metallo-beta-lactamases, n = 45 OXA-48, and eight isolates harboring two different enzymes), n = 239 carbapenem-resistant noncarbapenemase producers, and n = 275 carbapenem-susceptible strains. The STAR-Carba assay detected 657/661 (99.4%) carbapenemase producers from plate cultures, and 132/132 (100%) from positive blood cultures. Specificity resulted in 100% for carbapenem-susceptible strains, and 91.6% for carbapenem-resistant strains resulted negative for carbapenamase production with the routine methods used in this study. In this study, the MBT STAR-Carba assay proved to be a highly reliable method for the detection of carbapenemase-producing Enterobacterales, regardless of the enzyme family, and from both plate cultures and positive blood culture bottles.

Carbapenemase-producing Enterobacteriaceae in animals and methodologies for their detection

Carbapenemase-producing bacteria are difficult to treat and pose an important threat for public health. Detecting and identifying them can be a challenging and time-consuming task. Due to the recent rise in prevalence of infections with these organisms, there is an increased demand for rapid and accurate detection methods. This review describes and contrasts current methods used for the identification and detection of carbapenemase-producing bacteria to help control their spread in animal populations and along the food chain. The methods discussed include cultures used for screening clinical samples and primary isolation, susceptibility testing, culture-based and molecular confirmation tests. Advantages and disadvantages as well as limitations of the methods are discussed.

Phenotypic and Genotypic Characterization of Clinical Isolates Belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) Complex Isolated From Animals Treated at a Veterinary Hospital in Switzerland

Objectives: We investigated a collection of strains belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex obtained from a veterinary clinic with regard to their genetic relatedness, presence of antibiotic resistance genes and antimicrobial susceptibility profiles.

Methods: Fifty-eight ACB-complex strains from animals treated at a veterinary clinic between 2006 and 2017, and seven strains collected from the hospital environment during 2012 were analyzed. Assignment to sequence types (ST) and international complexes (IC) was done by multilocus sequence typing (MLST) according to the Pasteur scheme. Genes encoding carbapenemases, aminoglycoside-modifying enzymes, macrolide-, quinolone- and co-trimoxazole resistance genes, the ISAba1 element, virulence associated intI1 genes and plasmid associated toxin-antitoxin markers were identified by microarray. Genes encoding bla_OXA−51-like carbapenemases were amplified by PCR and sequenced. Susceptibility profiles were determined by disc diffusion or by broth microdilution.

Results: Among 50 A. baumannii isolates from animals, two predominant clones were observed linked to CC1 (n = 27/54% of the isolates) and CC25 (n = 14/28%), respectively. Strains of IC I harbored bla_OXA−69, aac(3′)-la, aadA1, sul1, intI1, and splA/T genes. Isolates belonging to CC25 possessed bla_OXA−64. Six (12%) isolates belonging to CC2 and carrying bla_OXA−66 were also noted. One isolate belonged to CC10 (bla_OXA−68), one to CC149 (bla_OXA−104), the remaining isolate was assigned to ST1220 and possessed bla_OXA−116. Of six environmental A. baumannii, four (66.7%) belonged to CC25 (bla_OXA−64), one (16.7%) to CC2 (bla_OXA−66) and one to CC3 (bla_OXA−71). Nine isolates (eight from animals and one environmental strain) were non-baumannii strains and did not harbor bla_OXA−51-like genes. None of the isolates carried bla_OXA−23, bla_OXA−48, or bla_OXA−58, and none were resistant to carbapenems.

Conclusions: Clonal lineages of the veterinary A. baumannii isolates in our collection are identical to those globally emerging in humans but do not harbor bla_OXA−23. A. baumannii CC25 may be specific for this particular veterinary clinic environment.

ESBL colonization and acquisition in a hospital population: The molecular epidemiology and transmission of resistance genes

A prospective cohort study (German Clinical Trial Registry, No. 00005273) was performed to determine pre-admission colonization rates, hospital acquisition risk factors, subsequent infection rates and colonization persistence including the respective molecular epidemiology and transmission rates of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (EPE). A total of 342 EPEs were isolated from rectal swabs of 1,334 patients on admission, at discharge and 6 months after hospitalization. Inclusion criteria were patients’ age > 18 years, expected length of stays > 48 hours, external referral. The EPEs were characterized by routine microbiological methods, a DNA microarray and ERIC-PCR. EPE colonization was found in 12.7 % of admitted patients, with the highest rate (23.8 %) in patients from nursing homes. During hospitalization, 8.1 % of the patients were de novo EPE colonized, and invasive procedures, antibiotic and antacid therapies were independent risk factors. Only 1/169 patients colonized on admission developed a hospital-acquired EPE infection. Escherichia coli was the predominant EPE (88.9 %), and 92.1% of the ESBL phenotypes could be related to CTX-M variants with CTX-M-1/15 group being most frequent (88.9%). A corresponding β-lactamase could not be identified in five isolates. Hospital-acquired EPE infections in patients colonized before or during hospitalization were rare. The diversity of the EPE strains was much higher than that of the underlying plasmids. In seven patients, transmission of the respective plasmid across different species could be observed indicating that the current strain-based surveillance approaches may underestimate the risk of inter-species transmission of resistance genes.

Fast, economic and simultaneous identification of clinically relevant Gram-negative species with multiplex real-time PCR

AIM

A newly designed multiplex real-time PCR (rt-PCR) was validated to detect four clinically relevant Gram-negative bacteria (Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae and Pseudomonas aeruginosa).

MATERIALS & METHODS

Serial dilutions of genomic DNA were used to determine the limit of detection. Colony PCR was performed with isolates of the four selected species and other species as negative controls. Isolates were characterized genotypically and phenotypically to evaluate the assay.

RESULTS

Specific signals of all target genes were detected with diluted templates comprising ten genomic equivalents. Using colony rt-PCR, all isolates of the target species were identified correctly. All negative control isolates were negative.

CONCLUSION

The genes gad, basC, khe and ecfX can reliably identify these four species via multiplex colony rt-PCR.

Detection of carbapenemases, AmpC and ESBL genes in Acinetobacter isolates from ICUs by DNA microarray

The accumulation of multiple inherent and acquired resistance mechanisms in Acinetobacter spp. results in emergence of "pandrug resistant" strains which is one of the major concerns in healthcare sectors worldwide. Surveillance of the carbapenemase/ extended-spectrum β-lactamases (ESBLs) genes in A. baumannii by phenotypic methods is challenging especially in developing countries, like Pakistan. In this context, a novel microarray (CT 103XL Check-MDR) assay was used for simultaneous detection of genes encoding clinically important carbapenemases and ESBLs. The results were compared with the phenotypic methods including MHT, Rapidec Carba NP, EDTA+DDST and Rosco (KPC/MBL). The results of the microarray were also confirmed by PCR. All of the strains of A. baumannii (47) were resistant to imipenem and meropenem. Microarray and PCR results showed presence of OXA-23 in all the isolates of A. baumannii while 36.17% also harbored PER. Rosco kit test showed 100% sensitivity to detect carbapenemases but exhibited low specificity to classify them. Rapidec Carba NP test has 100% sensitivity and specificity to detect the carbapenemases when compared with microarray. Sensitivity and specificity of microarray assay were 100% for bla-genes in comparison to PCR. This reveals that Check-MDR CT103 XL assay is an accurate method for the identification of ESBLs and carbapenemase genes in A. baumannii in comparison to the other methods.

Antimicrobial resistance in Enterobacteriaceae from healthy broilers in Egypt: emergence of colistin-resistant and extended-spectrum β-lactamase-producing Escherichia coli

Background

Poultry remains one of the most important reservoir for zoonotic multidrug resistant pathogens. The global rise of antimicrobial resistance in Gram-negative bacteria is of reasonable concern and demands intensified surveillance.

Methods

In 2016, 576 cloacal swabs were collected from 48 broiler farms located in five governorates in northern Egypt. Isolates of Enterobacteriaceae could be cultivated on different media and were identified by MALDI-TOF MS and PCR. Escherichia coli isolates were genotyped by DNA-microarray-based assays. The antimicrobial susceptibility to 14 antibiotics was determined and resistance-associated genes were detected. The VITEK-2 system was applied for phenotypical confirmation of extended-spectrum β-lactamase-producing isolates. The determination of colistin resistance was carried out phenotypically using E-test and genotypically using PCR for detection of the mcr-1 gene.

Results

Out of 576 samples, 72 representatives of Enterobacteriaceae were isolated and identified as 63 E. coli (87.5%), 5 Enterobacter cloacae (6.9%), 2 Klebsiella pneumoniae (2.8%) and 2 Citrobacter spp. (2.8%). Seven out of 56 cultivated E. coli (12.5%) were confirmed as ESBL-producing E. coli and one isolate (1.8%) as ESBL/carbapenemase-producing E. coli. Five out of 63 E. coli isolates (7.9%) recovered from different poultry flocks were phenotypically resistant to colistin and harboured mcr-1 gene.

Conclusions

This is the first study reporting colistin resistance and emergence of multidrug resistance in Enterobacteriaceae isolated from healthy broilers in the Nile Delta region, Egypt. Colistin-resistant E. coli in poultry is of public health significance. The global rise of ESBL- and carbapenemase-producing Gram-negative bacteria demands intensified surveillance. ESBL-producing E. coli in poultry farms in Egypt are of major concern that emphasizes the possibility of spread of such strains to humans. The results also reinforce the need to develop strategies and to implement specific control procedures to reduce the use of antibiotics.

Current antimicrobial susceptibility testing for beta-lactamase-producing Enterobacteriaceae in clinical settings

The worldwide prevalence of beta-lactamase-producing Enterobacteriaceae (BL-E) is increasing. Bacterial infections involving ESBLs can be more difficult to treat because of antibiotic resistance, as there are fewer effective antibiotics left to be used. Moreover, treatment failure is often observed. Thus, quick and accurate identification of β-lactamases is imperative to minimize it. This review article describes most commonly used phenotypic techniques and molecular methods for the detection of ESBLs, acquired AmpC β-lactamases, and carbapenemases produced by Enterobacteriaceae. Phenotypic detection tests remain useful and relevant in clinical laboratories while molecular diagnostic methods are less affordable, more technically demanding, and not standardized. Molecular methods could be used to speed up results of bacterial antibiotic resistance or to clarify the results of phenotypic β-lactamases confirmation tests.

Prevalence of carbapenemase-producing organisms at the Kidney Center of Rawalpindi (Pakistan) and evaluation of an advanced molecular microarray-based carbapenemase assay

AIM

A DNA microarray-based assay for the detection of antimicrobial resistance (AMR) genes was used to study carbapenemase-producing organisms at the Kidney Center of Rawalpindi, Pakistan.

METHODS

The evaluation of this assay was performed using 97 reference strains with confirmed AMR genes. Testing of 7857 clinical samples identified 425 Gram-negative bacteria out of which 82 appeared carbapenem resistant. These isolates were analyzed using VITEK-2 for phenotyping and the described AMR assay for genotyping.

RESULTS

The most prevalent carbapenemase gene was blaNDM and in 12 isolates we detected two carbapenemase genes (e.g., blaNDM/blaOXA-48).

CONCLUSION

Our prevalence data from Pakistan show that - as in other parts of the world - carbapenemase-producing organisms with different underlying resistance mechanisms are emerging, and this warrants intensified and constant surveillance.

Development of a panel of recombinase polymerase amplification assays for detection of common bacterial urinary tract infection pathogens

AIMS

To develop and evaluate the performance of a panel of isothermal real-time recombinase polymerase amplification (RPA) assays for detection of common bacterial urinary tract infection (UTI) pathogens.

METHODS AND RESULTS

The panel included RPAs for Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa and Enterococcus faecalis. All five RPAs required reaction times of under 12 min to reach their lower limit of detection of 100 genomes per reaction or less, and did not cross-react with high concentrations of nontarget bacterial genomic DNA. In a 50-sample retrospective clinical study, the five-RPA assay panel was found to have a specificity of 100% (95% CI, 78-100%) and a sensitivity of 89% (95% CI, 75-96%) for UTI detection.

CONCLUSIONS

The analytical and clinical validity of RPA for the rapid and sensitive detection of common UTI pathogens was established.

SIGNIFICANCE AND IMPACT OF THE STUDY

Rapid identification of the causative pathogens of UTIs can be valuable in preventing serious complications by helping avoid the empirical treatment necessitated by traditional urine culture's 48-72-h turnaround time. The routine and widespread use of RPA to supplement or replace culture-based methods could profoundly impact UTI management and the emergence of multidrug-resistant pathogens.

Pseudomonas aeruginosa-producing Metallo-β-lactamases (VIM, IMP, SME, and AIM) in the Clinical Isolates of Intensive Care Units, a University Hospital in Isfahan, Iran

Background:

Pseudomonas aeruginosa is a severe challenge for antimicrobial therapy, due to the chromosomal mutations or exhibition of intrinsic resistance to various antimicrobial agents such as most β-lactams. We undertook this study to evaluate the existence of SME, IMP, AIM, and VIM metallo-β-lactamases (MBL) encoding genes among P. aeruginosa strains isolated from Intensive Care Unit (ICU) patients in Al-Zahra Hospital in Isfahan, Iran.

Materials and Methods:

In a retrospective cross-sectional study that was conducted between March 2012 and April 2013, a total of 48 strains of P. aeruginosa were collected from clinical specimens of bedridden patients in ICU wards. Susceptibility test was performed by disc diffusion method. All of the meropenem-resistant strains were subjected to modified Hodge test for detection of carbapenemases. Multiplex polymerase chain reaction was performed for detection of blaVIM, blaIMP, blaAIM, and blaSME genes.

Results:

In disk diffusion method, imipenem and meropenem showed the most and colistin the least resistant antimicrobial agents against P. aeruginosa strains. Of the 48 isolates, 36 (75%) were multidrug resistant (MDR). Amplification of β-lactamase genes showed the presence of blaVIM genes in 7 (%14.6) strains and blaIMP genes in 15 (31.3%) strains. All of the isolates were negative for blaSME and blaAIM genes. We could not find any statistically significant difference among the presence of this gene and MDR positive, age, or source of the specimen.

Conclusion:

As patients with infections caused by MBL-producing bacteria are at an intensified risk of treatment failure, fast determination of these organisms is necessary. Our findings may provide useful insights in replace of the appropriate antibiotics and may also prevent MBLs mediated resistance problem.

Occurrence of Salmonella enterica and Escherichia coli in raw chicken and beef meat in northern Egypt and dissemination of their antibiotic resistance markers

BACKGROUND

The global incidence of foodborne infections and antibiotic resistance is recently increased and considered of public health concern. Currently, scarcely information is available on foodborne infections and ESBL associated with poultry and beef meat in Egypt.

METHODS

In total, 180 chicken and beef meat samples as well as internal organs were collected from different districts in northern Egypt. The samples were investigated for the prevalence and antibiotic resistance of Salmonella enterica serovars and Escherichia coli. All isolates were investigated for harbouring class 1 and class 2 integrons.

RESULTS

Out of 180 investigated samples 15 S. enterica (8.3%) and 21 E. coli (11.7%) were isolated and identified. S. enterica isolates were typed as 9 S. Typhimurium (60.0%), 3 S. Paratyphi A (20.0%), 2 S. Enteritidis (13.3%) and 1 S. Kentucky (6.7%). Twenty-one E. coli isolates were serotyped into O1, O18, O20, O78, O103, O119, O126, O145, O146 and O158. The phenotypic antibiotic resistance profiles of S. enterica serovars to ampicillin, cefotaxime, cefpodoxime, trimethoprim/sulphamethoxazole and tetracycline were 86.7, 80.0, 60.0, 53.3 and 40.0%, respectively. Isolated E. coli were resistant to tetracycline (80.9%), ampicillin (71.4%), streptomycin, trimethoprim/sulphamethoxazole (61.9% for each) and cefotaxime (33.3%). The dissemination of genes coding for ESBL and AmpC β-lactamase in S. enterica isolates included bla_CTX-M (73.3%), bla_TEM (73.3%) and bla_CMY (13.3%). In E. coli isolates bla_TEM, bla_CTX-M and bla_OXA were identified in 52.4, 42.9 and 14.3%, respectively. The plasmid-mediated quinolone resistance genes identified in S. enterica were qnrA (33.3%), qnrB (20.0%) and qnrS (6.7%) while qnrA and qnrB were detected in 33.3% of E. coli isolates. Class 1 integron was detected in 13.3% of S. enterica and in 14.3% of E. coli isolates. Class 2 integron as well as the colistin resistance gene mcr-1 was not found in any of E. coli or S. enterica isolates.

CONCLUSIONS

This study showed high prevalence of S. enterica and E. coli as foodborne pathogens in raw chicken and beef meat in Nile Delta, Egypt. The emergence of antimicrobial resistance in S. enterica and E. coli isolates is of public health concern in Egypt. Molecular biological investigation elucidated the presence of genes associated with antibiotic resistance as well as class 1 integron in S. enterica and E. coli.

Epidemiology of transmissible diseases: Array hybridization and next generation sequencing as universal nucleic acid-mediated typing tools

The magnitude of interest in the epidemiology of transmissible human diseases is reflected in the vast number of tools and methods developed recently with the expressed purpose to characterize and track evolutionary changes that occur in agents of these diseases over time. Within the past decade a new suite of such tools has become available with the emergence of the so-called "omics" technologies. Among these, two are exponents of the ongoing genomic revolution. Firstly, high-density nucleic acid probe arrays have been proposed and developed using various chemical and physical approaches. Via hybridization-mediated detection of entire genes or genetic polymorphisms in such genes and intergenic regions these so called "DNA chips" have been successfully applied for distinguishing very closely related microbial species and strains. Second and even more phenomenal, next generation sequencing (NGS) has facilitated the assessment of the complete nucleotide sequence of entire microbial genomes. This technology currently provides the most detailed level of bacterial genotyping and hence allows for the resolution of microbial spread and short-term evolution in minute detail. We will here review the very recent history of these two technologies, sketch their usefulness in the elucidation of the spread and epidemiology of mostly hospital-acquired infections and discuss future developments.

The Changing Role of the Clinical Microbiology Laboratory in Defining Resistance in Gram-negatives

The evolution of resistance in Gram-negatives has challenged the clinical microbiology laboratory to implement new methods for their detection. Multidrug-resistant strains present major challenges to conventional and new detection methods. More rapid pathogen identification and antimicrobial susceptibility testing have been developed for use directly on specimens, including fluorescence in situ hybridization tests, automated polymerase chain reaction systems, microarrays, mass spectroscopy, next-generation sequencing, and microfluidics. Review of these methods shows the advances that have been made in rapid detection of resistance in cultures, but limited progress in direct detection from specimens.

Screening for carbapenem-resistant Enterobacteriaceae: Who, When, and How?

The global spread of carbapenem-resistant Enterobacteriaceae (CRE) has been fostered by the lack of preemptive screening of patients in healthcare facilities that could prevent patient-to-patient transmission. Outbreaks of CRE infections have led some institutions to implement rigorous screening programs, although controlled comparative data are frequently lacking. Resource limitations and uncertainty regarding the optimal approach has kept many facilities from enacting more active routine surveillance policies that could reduce the prevalence of CRE. The ideal population to target for screening, the frequency of testing, and the preferred test method are components of surveillance programs that remain open to debate. This review discusses the rationale for different screening policies in use and the performance characteristics of laboratory methods available to detect CRE carriage.

Current methods for the identification of carbapenemases

Detection of carbapenemases in clinical microbiology labs is a challenging issue. Comparison of the results of susceptibility testing with the breakpoint values of carbapenems is the first step in the screening of carbapenemase producers. To date, screening of carbapenemase-producing (CP) bacteria has been mostly performed by a selective medium. Although these media are practical for the detection of most CP isolates, the inoculated plates have to be incubated overnight. Subsequently, we need the confirmation of the carbapenemase producers present in the culture medium by additional testing [e.g. inhibition studies with liquid or solid media, modified Hodge test (MHT), or gradient strips], which can take up to another 48 hours. Despite the lack of discrimination between the three different classes of carbapenemases (KPC, MBL and OXA) and difficulties in the interpretation of the results, the MHT is usually deemed as the phenotypic reference method for the confirmation of carbapenemase production. Molecular techniques, such as real-time polymerase chain reaction (PCR) assays, in contrast to phenotypic methods that are very time consuming, are faster and allow for the quick identification of carbapenemase genes. These techniques can detect and characterize carbapenemases, including NDM- and KPC-mediated resistance, which is critical for epidemiological investigations. The aim of this review is to gather a summary of the available methods for carbapenemase detection and describe the strengths and weaknesses of each method.

The occurrence of ESBL-producing Escherichia coli carrying aminoglycoside resistance genes in urinary tract infections in Saudi Arabia

Background

The infection and prevalence of extended-spectrum β-lactamases (ESBLs) is a worldwide problem, and the presence of ESBLs varies between countries. In this study, we investigated the occurrence of plasmid-mediated ESBL/AmpC/carbapenemase/aminoglycoside resistance gene expression in Escherichia coli using phenotypic and genotypic techniques.

Methods

A total of 58 E. coli isolates were collected from hospitals in the city of Makkah and screened for the production of ESBL/AmpC/carbapenemase/aminoglycoside resistance genes. All samples were subjected to phenotypic and genotypic analyses. The antibiotic susceptibility of the E. coli isolates was determined using the Vitek-2 system and the minimum inhibitory concentration (MIC) assay. Antimicrobial agents tested using the Vitek 2 system and MIC assay included the expanded-spectrum (or third-generation) cephalosporins (e.g., cefoxitin, cefepime, aztreonam, cefotaxime, ceftriaxone, and ceftazidime) and carbapenems (meropenem and imipenem). Reported positive isolates were investigated using genotyping technology (oligonucleotide microarray-based assay and PCR). The genotyping investigation was focused on ESBL variants and the AmpC, carbapenemase and aminoglycoside resistance genes. E. coli was phylogenetically grouped, and the clonality of the isolates was studied using multilocus sequence typing (MLST).

Results

Our E. coli isolates exhibited different levels of resistance to ESBL drugs, including ampicillin (96.61%), cefoxitin (15.25%), ciprofloxacin (79.66%), cefepime (75.58%), aztreonam (89.83%), cefotaxime (76.27%), ceftazidime (81.36%), meropenem (0%) and imipenem (0%). Furthermore, the distribution of ESBL-producing E. coli was consistent with the data obtained using an oligonucleotide microarray-based assay and PCR genotyping against genes associated with β-lactam resistance. ST131 was the dominant sequence type lineage of the isolates and was the most uropathogenic E. coli lineage. The E. coli isolates also carried aminoglycoside resistance genes.

Conclusions

The evolution and prevalence of ESBL-producing E. coli may be rapidly accelerating in Saudi Arabia due to the high visitation seasons (especially to the city of Makkah). The health authority in Saudi Arabia should monitor the level of drug resistance in all general hospitals to reduce the increasing trend of microbial drug resistance and the impact on patient therapy.

CHROMagar mSuperCARBA performance in carbapenem-resistant Enterobacteriaceae isolates characterized at molecular level and routine surveillance rectal swab specimens

Performance of the CHROMagar mSuperCARBA media was assessed in both well-characterized carbapenem-resistant Enterobacteriaceae (n=52) and routine surveillance rectal swab specimens (n=211). Limit of detection ranged between 10¹ and 10²CFU/mL except for OXA-48 producers with low-carbapenem MICs (10⁶CFU/mL). High sensitivity (100%) and specificity (100%) were obtained with rectal swabs.

Surveillance of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in Dairy Cattle Farms in the Nile Delta, Egypt

Introduction: Industrial livestock farming is a possible source of multi-resistant Gram-negative bacteria, including producers of extended spectrum beta-lactamases (ESBLs) conferring resistance to 3rd generation cephalosporins. Limited information is currently available on the situation of ESBL producers in livestock farming outside of Western Europe. A surveillance study was conducted from January to May in 2014 in four dairy cattle farms in different areas of the Nile delta, Egypt.

Materials and Methods: In total, 266 samples were collected from 4 dairy farms including rectal swabs from clinically healthy cattle (n = 210), and environmental samples from the stalls (n = 56). After 24 h pre-enrichment in buffered peptone water, all samples were screened for 3rd generation cephalosporin-resistant Escherichia coli using Brilliance™ ESBL agar. Suspected colonies of putatively ESBL-producing E. coli were sub-cultured and subsequently genotypically and phenotypically characterized. Susceptibility testing using the VITEK-2 system was performed. All suspect isolates were genotypically analyzed using two DNA-microarray based assays: CarbDetect AS-1 and E. coli PanType AS-2 kit (ALERE). These tests allow detection of a multitude of genes and their alleles associated with resistance toward carbapenems, cephalosporins, and other frequently used antibiotics. Serotypes were determined using the E. coli SeroGenotyping AS-1 kit (ALERE).

Results: Out of 266 samples tested, 114 (42.8%) ESBL-producing E. coli were geno- and phenotypically identified. 113 of 114 phenotypically 3rd generation cephalosporin-resistant isolates harbored at least one of the ESBL resistance genes covered by the applied assays [blaCTX-M15 (n = 105), blaCTX-M9 (n = 1), blaTEM (n = 90), blaSHV (n = 1)]. Alarmingly, the carbapenemase genes blaOXA-48 (n = 5) and blaOXA-181 (n = 1) were found in isolates that also were phenotypically resistant to imipenem and meropenem. Using the array-based serogenotyping method, 66 of the 118 isolates (55%) could be genotypically assigned to O-types.

Conclusion: This study is considered to be a first report of the high prevalence of ESBL-producing E. coli in dairy farms in Egypt. ESBL-producing E. coli isolates with different underlying resistance mechanisms are common in investigated dairy cattle farms in Egypt. The global rise of ESBL- and carbapenemase-producing Gram-negative bacteria is a big concern, and demands intensified surveillance.

Global Dissemination of Carbapenemase-Producing Klebsiella pneumoniae: Epidemiology, Genetic Context, Treatment Options, and Detection Methods

The emergence of carbapenem-resistant Gram-negative pathogens poses a serious threat to public health worldwide. In particular, the increasing prevalence of carbapenem-resistant Klebsiella pneumoniae is a major source of concern. K. pneumoniae carbapenemases (KPCs) and carbapenemases of the oxacillinase-48 (OXA-48) type have been reported worldwide. New Delhi metallo-β-lactamase (NDM) carbapenemases were originally identified in Sweden in 2008 and have spread worldwide rapidly. In this review, we summarize the epidemiology of K. pneumoniae producing three carbapenemases (KPCs, NDMs, and OXA-48-like). Although the prevalence of each resistant strain varies geographically, K. pneumoniae producing KPCs, NDMs, and OXA-48-like carbapenemases have become rapidly disseminated. In addition, we used recently published molecular and genetic studies to analyze the mechanisms by which these three carbapenemases, and major K. pneumoniae clones, such as ST258 and ST11, have become globally prevalent. Because carbapenemase-producing K. pneumoniae are often resistant to most β-lactam antibiotics and many other non-β-lactam molecules, the therapeutic options available to treat infection with these strains are limited to colistin, polymyxin B, fosfomycin, tigecycline, and selected aminoglycosides. Although, combination therapy has been recommended for the treatment of severe carbapenemase-producing K. pneumoniae infections, the clinical evidence for this strategy is currently limited, and more accurate randomized controlled trials will be required to establish the most effective treatment regimen. Moreover, because rapid and accurate identification of the carbapenemase type found in K. pneumoniae may be difficult to achieve through phenotypic antibiotic susceptibility tests, novel molecular detection techniques are currently being developed.

Multisite Evaluation of Cepheid Xpert Carba-R Assay for Detection of Carbapenemase-Producing Organisms in Rectal Swabs

Rapid identification of patients who are colonized with carbapenemase-producing organisms (CPO) is included in multiple national guidelines for containment of these organisms. In a multisite study, we evaluated the performance of the Cepheid Xpert Carba-R assay, a qualitative diagnostic test that was designed for the rapid detection and differentiation of the bla_KPC, bla_NDM, bla_VIM, bla_OXA-48, and bla_IMP-1 genes from rectal swab specimens. A double rectal swab set was collected from 383 patients admitted at four institutions (2 in the United States, 1 in the United Kingdom, 1 in Spain). One swab was used for reference culture (MacConkey broth containing 1 mg/liter of meropenem and subcultured to a MacConkey agar plate with a 10-μg meropenem disk) and for sequencing of DNA obtained from carbapenem-nonsusceptible isolates for carbapenemase identification. The other swab was used for the Xpert Carba-R assay. In addition to the clinical rectal swabs, 250 contrived specimens (108 well-characterized CPO and 142 negative controls spiked onto negative rectal swabs) were tested. Overall, 149/633 (23.5%) samples were positive by the Xpert Carba-R assay. In 6 samples, multiple targets were detected (4 VIM/OXA-48, 1 IMP-1/NDM, and 1 NDM/KPC). The Xpert Carba-R assay detected 155 targets (26 IMP-1, 30 VIM, 27 NDM, 33 KPC, 39 OXA-48) within a time range of 32 to 48 min. The sensitivity, specificity, and positive and negative predictive values of the Xpert Carba-R assay compared to those of the reference culture and sequencing results were 96.6% (95% confidence interval [CI], 92.2% to 98.9%), 98.6% (95% CI, 97.1% to 99.4%), 95.3%, and 99.0%, respectively. The Cepheid Xpert Carba-R assay is an accurate and rapid test to identify rectal colonization with CPO, which can guide infection control programs to limit the spread of these organisms.

Recent advances in the laboratory detection of carbapenemase-producing Enterobacteriaceae

Carbapenemase-producing Enterobacteriaceae (CPE), mainly Klebsiella pneumoniae and Escherichia coli, have been increasing rapidly on a global scale and are considered to be significant health threats. The most common carbapenemases are KPCs, NDMs, OXA-48-like, IMPs and VIMs but their distribution and prevalence differs between countries. The accurate, simple, cost effective and rapid detection of carbapenemases in clinical laboratories is an important initial step to control the spread of CPE within institutions. The diversity of carbapenemases in general, has challenged a simple approach for the detection of most types of CPE. This article summarizes the current and describes newer techniques available for the detection of carbapenemases among Enterobacteriaceae. The authors also provide a simplified approach for the accurate and rapid detection of CPEs that can easily be implemented in a clinical diagnostic laboratory.

Carbapenemase-producing Enterobacteriaceae: a 2-year surveillance in a hospital in Iaşi, Romania

Aim: Limited information is currently available about the prevalence of carbapenemase-producing Enterobacteriaceae (CPE) in Romania. Materials & methods: Routine tests of 1,993 clinical isolates at a hospital in Iaşi yielded 46 isolates that were resistant to carbapenems. All 46 isolates were phenotypically and genotypically analyzed using VITEK-2 and DNA microarray-based assays. Results: Isolates were assigned to Klebsiella pneumoniae and Enterobacter cloacae. For 39 isolates, carbapenem resistance was confirmed and 37 harbored at least one carbapenem resistance gene. Two isolates were probably resistant due to AmpC β-lactamases in combination with a porin loss. The overall concordance between detected phenotype and genotype was 95%. Conclusion: Our data show that carbapenemase-producing isolates with different underlying resistance mechanisms are still rare in Iaşi, but the global rise of CPE warrants intensified surveillance.

Assessment of species and antimicrobial resistance among Enterobacteriaceae isolated from mallard duck faeces

Mallard ducks have demonstrated to be a likely reservoir for zoonotic E. coli strains; thus, it is possible that these ducks could also act as a reservoir for other Enterobacteriaceae members. The present study was initiated to evaluate the species distribution of Enterobacteriaceae other than E. coli in 175 fresh faecal samples collected from a population of mallard ducks. Sixty-four samples displayed detectable colonies of Enterobacteriaceae (excluding E. coli), which resulted in 75 pulsed-field gel electrophoresis (PFGE) types. Seventy-five single representatives of each PFGE type were subjected to identification with API 32NE and MALDI TOF MS systems due to the practical difficulties in species differentiation of Enterobacteriaceae. Those isolated were found to be from nine genera: Buttiauxella (15 %), Citrobacter (5 %), Enterobacter (32 %), Hafnia (1 %), Leclercia (1 %), Pantoea (7 %), Raoultella (21 %), Rahnella (7 %) and Serratia (11 %). Evaluation of antimicrobial resistance phenotypes using the disc method and detection of resistance genes using the microarray method revealed that these microbes possess resistance to β-lactams, aminoglycosides, macrolides, quinolones, rifamycine, sulphonamides, streptogramins and diaminopyrimidines. In conclusion, mallard ducks harbour a variety of non-pathogenic and pathogenic Enterobacteriaceae species like Enterobacter cloacae and Enterobacter amnigenus in their intestine and could act as a reservoir of resistant Enterobacteriaceae.

Current preventive measures for health-care associated surgical site infections: a review

Healthcare-associated infections (HAIs) continue to be a tremendous issue today. It is estimated 1.7 million HAIs occur per year, and cost the healthcare system up to $45 billion annually. Surgical site infections (SSIs) alone account for 290,000 of total HAIs and approximately 8,000 deaths. In today's rapidly changing world of medicine, it is ever important to remain cognizant of this matter and its impact both globally and on the individual lives of our patients. This review aims to impress upon the reader the unremitting significance of HAIs in the daily practice of medicine. Further, we discuss the etiology of HAIs and review successful preventive measures that have been demonstrated in the literature. In particular, we highlight preoperative, intraoperative, and postoperative interventions to combat SSIs. Finally, we contend that current systems in place are often insufficient, and emphasize the benefits of institution-wide adoption of multiple preventive interventions. We hope this concise update and review can inspire additional dialogue for the continuing progress towards improving patient care and patient lives.