Genetic methods for detection of antibiotic resistance: focus on extended-spectrum β-lactamases

Prevalence and molecular characterization of ESBL-producing Escherichia coli isolated from broiler chicken and their respective farms environment in Malaysia

BACKGROUND

Extended spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) is an increasing public health threat. This study aimed to determine the prevalence and characterization of ESBL-producing Escherichia coli (E. coli) isolated from broiler chicken and their farm environment, in Kelantan Malaysia.

METHODS

Escherichia coli was isolated from 453 collected samples, including 210 cloacal swabs and 243 environmental samples. The antimicrobial susceptibility profile of the E. coli isolates was assessed for sixteen antibiotics using the disc diffusion method. The E. coli isolates were evaluated for phenotypic ESBL production using modified double disc synergy. After extraction of genomic DNA, ESBL resistance genes, phylogenetic group, and virulence genes were detected by PCR using appropriate primers. ESBL genes were further confirmed by sequencing. The molecular typing of E. coli strains was determined by Multilocus Sequence Typing (MLST).

RESULTS

A total of 93.8% (425/453) E. coli were isolated from the collected samples. Out of 334 E. coli isolates screened, 14.7% (49/334) were phenotypically ESBL producers. All the ESBL-EC were resistant to tetracycline, ciprofloxacin, and ampicillin. Thus, 100% of the ESBL-EC were multidrug resistant. Of the ESBL-EC 81.6% were positive for at least one ESBL encoding gene. The most prevalent ESBL gene detected was blaTEM (77.6%; 38/49) followed by blaCTX-M (32.7%; 16/49) and blaSHV (18.4%; 9/49). The majority of ESBL-EC belonged to phylogenic groups A followed by B1 accounting for 44.9% and 12.2%, respectively. The most frequently identified sequence types were ST10 (n = 3) and ST206 (n = 3). The most detected virulence genes in the E. coli isolates were astA (33.3%; 22/66) followed by iss (15.2%; 10/66).

CONCLUSIONS

Our results show both broiler chicken and their respective farms environment were reservoirs of multi-drug resistant ESBL-producing E. coli and ESBL resistance genes.

Phylotypic Profiling, Distribution of Pathogenicity Island Markers, and Antimicrobial Susceptibility of Escherichia coli Isolated from Retail Chicken Meat and Humans

Escherichia coli (E.coli) found in retail chicken meat could be causing a wide range of infections in humans and constitute a potential risk. This study aimed to evaluate 60 E. coli isolates from retail chicken meat (n = 34) and human urinary tract infections (UTIs, n = 26) for phylogenetic diversity, presence of pathogenicity island (PAI) markers, antimicrobial susceptibility phenotypes, and antimicrobial resistance genes, and to evaluate their biofilm formation capacity. In that context, confirmed E.coli isolates were subjected to phylogrouping analysis using triplex PCR, antimicrobial susceptibility testing using the Kirby–Bauer disc diffusion method; PAI distribution was investigated by using two multiplex PCRs. Most of the chicken isolates (22/34, 64.7%) were identified as commensal E. coli (A and B1), while 12 isolates (35.3%) were classified as pathogenic virulent E. coli (B2 and D). Similarly, the commensal group dominated in human isolates. Overall, 23 PAIs were detected in the chicken isolates; among them, 39.1% (9/23) were assigned to group B1, 34.8% (8/23) to group A, 4.34% (1/23) to group B2, and 21.7% (5/23) to group D. However, 25 PAIs were identified from the human isolates. PAI IV536 was the most prevalent (55.9%, 69.2%) PAI detected in both sources. In total, 37 (61.7%) isolates of the chicken and human isolates were biofilm producers. Noticeably, 100% of E. coli isolates were resistant to penicillin and rifamycin. Markedly, all E. coli isolates displayed multiple antibiotic resistance (MAR) phenotypes, and the multiple antibiotic resistance index (MARI) among E. coli isolates ranged between 0.5 and 1. Several antibiotic resistance genes (ARGs) were identified by a PCR assay; the sul2 gene was the most prevalent (38/60, 63.3%) from both sources. Interestingly, a significant positive association (r = 0.31) between biofilm production and resistance to quinolones by the qnr gene was found by the correlation analysis. These findings were suggestive of the transmission of PAI markers and antibiotic resistance genes from poultry to humans or humans to humans through the food chain. To avoid the spread of virulent and multidrug-resistant E. coli, intensive surveillance of retail chicken meat markets is required.

Bacterial profile of high-touch surfaces, leftover drugs and antiseptics together with their antimicrobial susceptibility patterns at University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia

Background

The hospital environment serves as a source of nosocomial infections, which pose a major therapeutic challenge. Although many bacteria species are common in hospital environments, their distribution, frequency, and antimicrobial susceptibility pattern from high-touch surfaces, leftover drugs, and antiseptics in different wards remain largely unknown. Hence, the aim of this study was to assess the magnitude and frequency of bacterial contaminants and their antimicrobial susceptibility patterns.

Methods

A total of 384 samples were collected from five selected wards and processed according to standard bacteriological procedures. Samples were collected from high-touch surface using swabs and inoculated on Blood agar, MacConkey agar, Chocolate agar and Mannitol salt agar plates, and incubated at 37 °C for 24 h. On the other hand, the leftover drugs and 80% ethanol samples were collected using sterile cotton swab immersed in sterile tryptone soy broth then inoculated on culture medias and incubated at 37 °C for 24 h. Identification of bacteria species was done using the morphological characteristics, Gram stain, and biochemical tests while antimicrobial susceptibility tests were done using modified Kirby-Bauer disk diffusion technique following the Clinical Laboratory Standards Institute 2021guidelines.

Results

Among the 384 samples processed, 102 (26.6%) were culture positive and a total of 114 bacterial isolates were identified. Gram-positive bacterial isolates were predominant, 64.9%, while Gram-negatives were 35.1%. The most frequently isolated bacteria were coagulase negative Staphylococci (38.6%) followed by S. aureus (13.2%) and P. aeruginosa (11.4%). On the other hand, the proportion of bacteria isolated from surgical ward, post-natal ward, orthopedic ward, trauma ward, and neonatal intensive care unit ward were 24.6, 21, 20.2, 18.4,15.8%, respectively. Sinks were mainly contaminated with Klebsiella species (81.8%) and A. baumannii (55.6%), while A. baumannii (22.2%) was the most contaminant for 80% ethanol. Gram-positive bacteria had significantly high resistance levels to penicillin (67.6%), cotrimoxazole (67.8%), and cefepime (80%). On the other hand, Gram-negative bacteria revealed the highest resistance levels to tetracycline (82.4%), amoxicillin-clavulanic acid (76.5%), cefepime (66.7%), ceftazidime (67.5%), and piperacillin (92.3%). Moreover, the proportion of multidrug resistant bacteria isolates was 44.7%.

Conclusions

Data of the present study showed that coagulase negative Staphylococci was the dominant bacterial isolates followed by S. aureus and P. aeruginosa. The proportion of multi-drug resistant bacteria isolates was relatively high. Therefore, appropriate infection prevention and control measures should be implemented.

From Sequence Data to Patient Result: A Solution for HIV Drug Resistance Genotyping With Exatype, End to End Software for Pol-HIV-1 Sanger Based Sequence Analysis and Patient HIV Drug Resistance Result Generation

Introduction:

With the rapid scale-up of antiretroviral therapy (ART) to treat HIV infection, there are ongoing concerns regarding probable emergence and transmission of HIV drug resistance (HIVDR) mutations. This scale-up has to lead to an increased need for routine HIVDR testing to inform the clinical decision on a regimen switch. Although the majority of wet laboratory processes are standardized, slow, labor-intensive data transfer and subjective manual sequence interpretation steps are still required to finalize and release patient results. We thus set out to validate the applicability of a software package to generate HIVDR patient results from raw sequence data independently.

Methods:

We assessed the performance characteristics of Hyrax Bioscience’s Exatype (a sequence data to patient result, fully automated sequence analysis software, which consolidates RECall, MEGA X and the Stanford HIV database) against the standard method (RECall and Stanford database). Exatype is a web-based HIV Drug resistance bioinformatic pipeline available at sanger.exatype.com. To validate the exatype, we used a test set of 135 remnant HIV viral load samples at the National HIV Reference Laboratory (NHRL).

Result:

We analyzed, and successfully generated results of 126 sequences out of 135 specimens by both Standard and Exatype software. Result production using Exatype required minimal hands-on time in comparison to the Standard (6 computation-hours using the standard method versus 1.5 Exatype computation-hours). Concordance between the 2 systems was 99.8% for 311,227 bases compared. 99.7% of the 0.2% discordant bases, were attributed to nucleotide mixtures as a result of the sequence editing in Recall. Both methods identified similar (99.1%) critical antiretroviral resistance-associated mutations resulting in a 99.2% concordance of resistance susceptibility interpretations. The Base-calling comparison between the 2 methods had Cohen’s kappa (0.97 to 0.99), implying an almost perfect agreement with minimal base calling variation. On a predefined dataset, RECall editing displayed the highest probability to score mixtures accurately 1 vs. 0.71 and the lowest chance to inaccurately assign mixtures to pure nucleotides (0.002–0.0008). This advantage is attributable to the manual sequence editing in RECall.

Conclusion:

The reduction in hands-on time needed is a benefit when using the Exatype HIV DR sequence analysis platform and result generation tool. There is a minimal difference in base calling between Exatype and standard methods. Although the discrepancy has minimal impact on drug resistance interpretation, allowance of sequence editing in Exatype as RECall can significantly improve its performance.

Molecular Characterization of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae Isolates Collected from Inanimate Hospital Environments in Addis Ababa, Ethiopia

INTRODUCTION

The hospital environment contributes to the spread of Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE), which are contributing to increased morbidity and mortality rates. The present study was carried out to detect environmental contamination, antimicrobial susceptibility testing of ESBL-PE, and to explore molecular characterization of ESBL encoding genes.

METHODS

A cross-sectional study was conducted within the intensive care units (ICUs) of Tikur Anbessa Specialized Hospital from June to July 2018. A total of 97 swabs were taken from high-contact inanimate surfaces near immediate patient environments. All isolates were cultured by using ESBL ChromoSelect Agar and identified with conventional bacteriological methods. Antimicrobial susceptibility testing was performed as recommended by Clinical and Laboratory Standards Institute. Combination disk test was used to confirm ESBL production, while molecular characterizations of ESBL genes were performed by polymerase chain reaction.

RESULTS

Out of 97 swabbed sample, 24 (24.7%) were confirmed as ESBL-PE. The most predominant ESBL-PE was from E. coli (41.7%) and K. pneumoniae (25%). The Pediatrics and Neonatal ICU (29.2%, 7/24) exhibited highest ESBL-PE. The most contaminated materials were bed linens (33.3%). Most of ESBL-PE isolates were resistant to ampicillin (100%) and ceftriaxone (91.7%). A low resistance level was recorded for amikacin (25%). Among ESBL-producing genes, bla_CTX-M (35.7%) was the most prevalent, followed by bla_TEM and bla_SHV gene 32.1% for each.

CONCLUSIONS

Appearance of ESBL-PE in ICUs environment is posing a serious threat to control healthcare associated infections. The high level of resistance shows the need of policies for devising infection control procedures and detection of ESBL-PE.

Prevalence of antibiotic resistance and virulent factors in nosocomial clinical isolates of Pseudomonas aeruginosa from Panamá

Background

Pseudomonas aeruginosa is an important causative agent of nosocomial infections. As pathogen, P. aeruginosa is of increasing clinical importance due to its ability to develop high-level multidrug resistance (MDR).

Methods

The aim of the present study was to better understand the intrinsic virulence of circulating strains of Pseudomonas aeruginosa, by surveying and characterizing the antibiotic resistance profiles and prevalence of virulence factors in 51 clinical isolates of P. aeruginosa obtained from children admitted to Hospital del Niño-Panamá during the period of October 2016 until March 2017. Antimicrobial susceptibilities were assessed by determining the minimum inhibitory concentration for 12 antibiotics against P. aeruginosa clinical isolates using the VITEK system (https://www.biomerieux.com). Additionally, all isolates were examined by Polymerase Chain Reaction (PCR) for the presence of components of the MexAB-OprM efflux pump system (mexABR) and pyoverdine receptor genes and betalactamases resistance genes (ESBL) using gene-specific primers.

Results

A total of 51 pyoverdine producing clinical isolates were analyzed, all of which expressed resistance genes such as genes of the MexAB-OprM efflux pump system (mexABR) and pyoverdine receptor genes (fpvA). Out of 51 MDR isolates, 22 were ESBL producers. The most common ESBL gene was blaTEM expressed by 43% of the isolates. The isolates tested in this study showed increased resistance to antibiotics in the following categories: (i) penicillins (ampicillin (69%), piperacillin (22%); (ii) pyrimethamines (trimethoprim, 65%); (iii) nitrofurans (nitrofurantoin, 63%), and (iv) third-generation cephalosporin cefotaxime (53%). These results underscore a high prevalence of MDR amongst clinical isolates from Panama.

Conclusions

The present study indicates that prevalence of BlaTEM-carrying strains is increasing with subsequent multidrug resistance in Panamá and as well reported worldwide. The virulent factors identified in this study provide valuable information regarding the prevalence of resistance genes and their potential impact on treatments that exploit the unique physiology of the pathogen. To prevent further spread of MDR, the proportions of resistant strains of Pseudomonas aeruginosa should be constantly evaluated on healthcare institutions of Panamá. More importantly, this information can be used to better understand the evolution and dissemination of strains hoping to prevent the development of resistance in Pseudomonas aeruginosa. Future studies quantifying the expression of these virulent genes will emphasize on the acquisition of multidrug resistance.

Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: recent reports

Extraintestinal pathogenic E. coli (ExPEC) are facultative pathogens that are part of the normal human intestinal flora. The ExPEC group includes uropathogenic E. coli (UPEC), neonatal meningitis E. coli (NMEC), sepsis-associated E. coli (SEPEC), and avian pathogenic E. coli (APEC). Virulence factors (VF) related to the pathogenicity of ExPEC are numerous and have a wide range of activities, from those related to bacteria colonization to those related to virulence, including adhesins, toxins, iron acquisition factors, lipopolysaccharides, polysaccharide capsules, and invasins, which are usually encoded on pathogenicity islands (PAIs), plasmids and other mobile genetic elements. Mechanisms underlying the dynamics of ExPEC transmission and the selection of virulent clones are still poorly understood and require further research. The time shift between colonization of ExPEC and the development of infection remains problematic in the context of establishing the relation between consumption of contaminated food and the appearance of first disease symptoms. What appears to be most difficult is to prove that ExPEC strains cause disease symptoms and to examine the mechanism of transition from the asymptomatic colonization of the intestines to the spreading of the bacteria outside the digestive system. A significant problem for researchers who are trying to ascribe ExPEC transmission to food, people or the environment is to draw the distinction between colonization of ExPEC and infection. Food safety is an important challenge for public health both at the production stage and in the course of its processing and distribution. Examination of the genetic similarity of ExPEC strains will allow to determine their origin from different sources. Many levels of genotyping have been proposed in which the typing of strains, plasmids and genes is compared in order to obtain a more complete picture of this complex problem. The aim of our study was to characterize E. coli strains isolated from humans, animals and food for the presence of bacterial genes encoding virulence factors such as toxins, and iron acquisition systems (siderophores) in the context of an increasing spread of ExPEC infections.

The Effects of β-Lactam Antibiotics on Surface Modifications of Multidrug-Resistant Escherichia coli: A Multiscale Approach

Possible multidrug-resistant (MDR) mechanisms of four resistant strains of Escherichia coli to a model β-lactam, ampicillin, were investigated using contact angle measurements of wettability, crystal violet assays of permeability, biofilm formation, fluorescence imaging, and nanoscale analyses of dimensions, adherence, and roughness. Upon exposure to ampicillin, one of the resistant strains, E. coli A5, changed its phenotype from elliptical to spherical, maintained its roughness and biofilm formation abilities, decreased its length and surface area, maintained its cell wall integrity, increased its hydrophobicity, and decreased its nanoscale adhesion to a model surface of silicon nitride. Such modifications are suggested to allow these cells to conserve energy during metabolic dormancy. In comparison, resistant strains E. coli D4, A9, and H5 elongated their cells, increased their roughness, increased their nanoscale adhesion forces, became more hydrophilic, and increased their biofilm formation upon exposure to ampicillin. These results suggest that these strains resisted ampicillin through biofilm formation that possibly introduces diffusion limitations to antibiotics. Investigations of how MDR bacterial cells modify their surfaces in response to antibiotics can guide research efforts aimed at designing more effective antibiotics and new treatment strategies for MDR bacterial infections.

Molecular Tools To Study Preharvest Food Safety Challenges

Preharvest food safety research and activities have advanced over time with the recognition of the importance and complicated nature of the preharvest phase of food production. In developed nations, implementation of preharvest food safety procedures along with strict monitoring and containment at various postharvest stages such as slaughter, processing, storage, and distribution have remarkably reduced the burden of foodborne pathogens in humans. Early detection and adequate surveillance of pathogens at the preharvest stage is of the utmost importance to ensure a safe meat supply. There is an urgent need to develop rapid, cost-effective, and point-of-care diagnostics which could be used at the preharvest stage and would complement postmortem and other quality checks performed at the postharvest stage. With newer methods and technologies, more efforts need to be directed toward developing rapid, sensitive, and specific methods for detection or screening of foodborne pathogens at the preharvest stage. In this review, we will discuss the molecular methods available for detection and molecular typing of bacterial foodborne pathogens at the farm. Such methods include conventional techniques such as endpoint PCR, real-time PCR, DNA microarray, and more advanced techniques such as matrix-assisted layer desorption ionization-time of flight mass spectrometry and whole-genome sequencing.

Molecular characterisation of Klebsiella oxytoca strains isolated from patients with antibiotic-associated diarrhoea

BACKGROUND AND STUDY AIM

Colitis is a common complication after treatment with antibiotics such as β-lactams, quinolones, and aminoglycosides. Recently, Klebsiella oxytoca has been implicated in this type of diarrhoea. The prevalence and characterisations of K. oxytoca isolated from patients with antibiotic-associated diarrhoea were investigated. The K. oxytoca isolates were also tested for cytotoxin production.

PATIENTS AND METHODS

This study was conducted from May 2011 to Dec 2013. Faecal samples were collected from hospitalised patients receiving antibiotic treatment. Initial cultivation was performed on specific media. The clinical isolates were confirmed by polymerase chain reaction (PCR) using the specific K. oxytoca polygalacturonase (pehX) gene. The double-disc diffusion test was used to detect extended-spectrum beta-lactamase (ESBL)-producing strains. Tracking of ESBL-encoding genes was performed via PCR. The organism was cultured on Hep-2 cell lines for cytotoxin production.

RESULTS

Out of 331 samples collected from patients, 40 were confirmed molecularly to be clinical isolates of K. oxytoca. Fourteen (35%) ESBL-producing strains were isolated using the double-disc diffusion method. Among the molecularly confirmed K. oxytoca isolates, seven (17.5%) tested positive for the blaSHV gene, 12 (30%) for blaTEM, 10 (25%) for blaCTX-M, three (7.5%) for blaOXA, nine (22.5%) for blaCTX-M-15, and seven (17.5%) for blaTEM-1. Five (12%) isolates showed cytotoxin activity below 30%, 12 (30%) strains showed moderate cytotoxin activity between 30% and 60%, and 23 (58%) strains showed cytotoxin activity ⩾60%.

CONCLUSIONS

The cytotoxin-producing K. oxytoca is found to be one of the causes of antibiotic-induced colitis. Discontinuing treatment and allowing normal intestinal flora to be established or prescribing appropriate medication after antibiogram can help patients with antibiotic-induced haemorrhagic colitis in a timely manner.

Dissemination of Extended-Spectrum β-Lactamases and Quinolone Resistance Genes Among Clinical Isolates of Uropathogenic Escherichia coli in Children

BACKGROUND

Urinary tract infection (UTI) is one of the most common childhood bacterial infections and Escherichia coli is the major pathogen. Producing β-lactamase enzymes are the most common mechanism of bacterial resistance.

OBJECTIVES

This study aimed to determine the prevalence of Extended-Spectrum β-Lactamases (ESBLs) and Quinolone Resistance (qnr) genes in E. coli strains isolated from UTIs.

MATERIALS AND METHODS

In this study, a total of 120 isolates of E. coli from urinary tract infections of the children were collected at Besat Hospital in Hamadan, Iran, from October 2010 to October 2011. The bacterial isolates were identified by standard biochemical methods. Antimicrobial susceptibilities were determined by disk diffusion method, and ESBLs-producing was confirmed phenotypically using the double-disk synergy (DDS) test. The presence and identification of ESBLs and qnr genes were determined by Polymerase Chain Reaction (PCR).

RESULTS

The highest sensitivity was seen to imipenem (96.7%), amikacin (92.5%), nitrofurantoin (93.3%), ofloxacin (81.7%), gentamicin norfloxacin (70.8%), and ciprofloxacin (79.2%). In contrast, the highest rate of resistance was seen to co-trimoxazole (77%) and nalidixic acid (40.9%). The results showed that 6 (2.18%) and 4 (1.12%) isolates of ESBL-producing E. coli were positive with respect to having qnrB and qnrS genes, respectively. No isolates was found to have qnrA.

CONCLUSIONS

CTX-M was the most prevalent ESBL genotype in uropathogenic E. coli (UPEC) isolated from UTI. In addition, a high frequency of qnr genes among ESBL-producing E. coli was identified in this study. In order to avoid treatment failures, we recommend using phenotypic and molecular methods to diagnose these enzymes and qnr genes.

Antibiotic consumption and its influence on the resistance in Enterobacteriaceae

Background

Increasing bacterial resistance to antibiotics is one of the most serious problems in current medicine. An important factor contributing to the growing prevalence of multiresistant bacteria is application of antibiotics. This study aimed at analyzing the development of resistance of Enterobacteriaceae to selected beta-lactam, fluoroquinolone and aminoglycoside antibiotics in the University Hospital Olomouc and assessing the effect of selection pressure of these antibiotics.

Methods

For the period between 1 January 2000 and 31 December 2011, resistance of Klebsiella pneumoniae, Escherichia coli, Enterobacter cloacae and Proteus mirabilis to third- and fourth-generation cephalosporins, meropenem, piperacillin/tazobactam, fluoroquinolones and aminoglycosides was retrospectively studied. For the assessment of selection pressure of antibiotics, a parameter of defined daily dose in absolute annual consumption (DDDatb) based on the ATC/DDD classification and in relative annual consumption (RDDDatb) as the number of defined daily doses per 100 bed-days was used. The relationship between frequency of strains resistant to a particular antibiotic and antibiotic consumption was assessed by linear regression analysis using Spearman’s correlation. The level of statistical significance was set at p < 0.05.

Results

A total of 113,027 isolates from the Enterobacteriaceae family were analyzed. There was a significant effect of selection pressure of the primary antibiotic in the following cases: piperacillin/tazobactam in Klebsiella pneumoniae, gentamicin in Klebsiella pneumoniae and Escherichia coli and amikacin in Escherichia coli and Enterobacter cloacae. Also, there was significant correlation between resistance to ceftazidime and consumption of piperacillin/tazobactam in Klebsiella pneumoniae and Escherichia coli. No relationship was found between consumption of third- and fourth-generation cephalosporins and resistance to ceftazidime or between fluoroquinolone consumption and resistance to ciprofloxacin.

Conclusion

The study showed the effects of both direct and indirect selection pressure on increasing resistance to gentamicin, amikacin, piperacillin/tazobactam and ceftazidime. Given the fact that no correlation was found between resistance to fluoroquinolones and consumption of either primary or secondary antibiotics, we assume that the increasing resistance to fluoroquinolones is probably due to circulation of resistance genes in the bacterial population and that this resistance was not affected by reduced use of these antibiotics.