Molecular Epidemiology, Antimicrobial Resistance, and Virulence Genes in Drug-Resistant Bacteria

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Mechanism and Evolution of Antibiotic Resistance".

Deadline for manuscript submissions: closed (29 February 2024) | Viewed by 19622

Special Issue Editor


E-Mail Website
Guest Editor
Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
Interests: medical bacteriology; whole-genome sequencing; antimicrobial resistance; molecular diagnostics

Special Issue Information

Dear Colleagues,

Antimicrobial resistance (AMR) is one of the most serious issues in human and veterinary medicine worldwide. AMR is a natural process wherein microorganisms, particularly bacteria, elicit certain resistance processes, receive resistant genes from other bacteria through horizontal gene transfer, and adapt to antibiotics. Antimicrobial-resistant microorganisms are present in humans, animals, food, plants, and the environment. The primary cause of AMR is the misuse and overuse of antibiotics and poor hygiene and sanitation in both humans and animals. Studies on the diversity, distribution, and persistence of drug-resistant and virulence genes in bacterial populations serve as useful tools for improving the understanding of AMR epidemiology. Therefore, we welcome studies on molecular epidemiology, AMR, and the molecular characterization of antibiotic-resistant and virulence genes in bacteria, which can contribute to the understanding of potential molecular, genetic, and environmental risk factors to the etiology, distribution, and prevention of diseases in healthcare facilities and farms.

Dr. Aunchalee Thanwisai
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Antibiotics is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular epidemiology
  • antimicrobial resistance
  • virulence genes
  • drug-resistant bacteria
  • antimicrobial activity

Published Papers (8 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

16 pages, 1431 KiB  
Article
Prevalence and Transmission of Extended-Spectrum Cephalosporin (ESC) Resistance Genes in Escherichia coli Isolated from Poultry Production Systems and Slaughterhouses in Denmark
by Meiyao Che, Tina Birk and Lisbeth Truelstrup Hansen
Antibiotics 2023, 12(11), 1602; https://doi.org/10.3390/antibiotics12111602 - 8 Nov 2023
Cited by 1 | Viewed by 1093
Abstract
The emergence of extended-spectrum cephalosporin (ESC)-resistant Escherichia coli is a global concern. This study aimed to assess the prevalence and transmission of ESC-resistant E. coli in the Danish broiler production system. Samples from two vertically integrated Production Systems (1 and 2) and two [...] Read more.
The emergence of extended-spectrum cephalosporin (ESC)-resistant Escherichia coli is a global concern. This study aimed to assess the prevalence and transmission of ESC-resistant E. coli in the Danish broiler production system. Samples from two vertically integrated Production Systems (1 and 2) and two slaughterhouses (A and B) were analyzed (n = 943) for the occurrence of ESC-resistant E. coli from 2015 to 2018. ESC-resistant E. coli isolates were whole-genome sequenced (WGS) for characterization of the multi-locus sequence type (MLST), antibiotic resistance genes, virulence genes, and plasmid replicon types. An ad hoc core genome (cg) MLST based on 2513 alleles was used to examine the genetic relatedness among isolates. The prevalence of ESC-resistant E. coli in the conventional Production System 1 was 2.7%, while in Production System 2 the prevalence was 26.7% and 56.5% for samples from the conventional and organic production, respectively. The overall prevalence of ESC-resistant E. coli in broiler thigh and fecal samples ranged from 19.3% in Slaughterhouse A to 22.4% in Slaughterhouse B. In total, 162 ESC-resistant E. coli were isolated and shown to belong to 16 different sequence types (STs). The most prevalent STs were ST2040 (n = 85) and ST429 (n = 22). Seven ESC resistance genes were detected: blaCMY-2 (n = 119), blaTEM-52B (n = 16), blaCTX-M-1 (n = 5), blaTEM-52C (n = 3), blaCTX-M-14 (n = 1), blaSHV-12 (n = 1), and up-regulation of ampC (n = 16), with an unknown resistance gene in one isolate (n = 1). The carriage of blaCMY-2 in 119 isolates was primarily associated with IncI1 (n = 87), and IncK plasmids (n = 31). Highly similar blaCMY-2 carrying E. coli isolates from ST429 were found in production systems as well as in slaughterhouses. In conclusion, findings from this study indicate that ESC-resistant E. coli are transferred vertically from farms in the production systems to slaughterhouses with the potential to enter the food supply. Full article
Show Figures

Figure 1

12 pages, 7417 KiB  
Article
Clonal, Plasmidic and Genetic Diversity of Multi-Drug-Resistant Enterobacterales from Hospitalized Patients in Tripoli, Libya
by Nada Elgriw, Véronique Métayer, Antoine Drapeau, Pauline François, Sana Azaiez, Maha Mastouri, Hajer Rhim, Adam Elzagheid, Najeeb Soufiyah, Jean-Yves Madec, Cherifa Chaouch, Wejdene Mansour and Marisa Haenni
Antibiotics 2023, 12(9), 1430; https://doi.org/10.3390/antibiotics12091430 - 10 Sep 2023
Viewed by 1369
Abstract
Resistance to extended-spectrum cephalosporins (ESC) and carbapenems in Enterobacterales is a major issue in public health. Carbapenem resistance in particular is associated with increased morbidity and mortality. Moreover, such resistance is often co-harbored with resistance to non-beta-lactam antibiotics, and pathogens quickly become multi-drug-resistant [...] Read more.
Resistance to extended-spectrum cephalosporins (ESC) and carbapenems in Enterobacterales is a major issue in public health. Carbapenem resistance in particular is associated with increased morbidity and mortality. Moreover, such resistance is often co-harbored with resistance to non-beta-lactam antibiotics, and pathogens quickly become multi-drug-resistant (MDR). Only a few studies have been published on AMR in Libyan hospitals, but all reported worrisome results. Here, we studied 54 MDR isolates that were collected from 49 patients at the Tripoli University Hospital between 2019 and 2021. They were characterized using phenotypic methods, PCR and PFGE, and a sub-set of isolates were short- and long-read whole-genome sequenced. The results showed the frequent occurrence of Klebsiella pneumoniae (49/54), among which several high-risk clones were responsible for the spread of resistance, namely, ST11, ST17, ST101 and ST147. ESC and carbapenem resistance was due to a wide variety of enzymes (CTX-M, OXA-48, NDM, KPC), with their corresponding genes carried by different plasmids, including IncF-IncHI2 and IncF-IncR hybrids. This study highlights that implementation of infection prevention, control and surveillance measures are needed in Libya to fight against AMR. Full article
Show Figures

Figure 1

11 pages, 532 KiB  
Article
Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Food-Producing Animals in Tamaulipas, Mexico
by Antonio Mandujano, Diana Verónica Cortés-Espinosa, José Vásquez-Villanueva, Paulina Guel, Gildardo Rivera, Karina Juárez-Rendón, Wendy Lizeth Cruz-Pulido, Guadalupe Aguilera-Arreola, Abraham Guerrero, Virgilio Bocanegra-García and Ana Verónica Martínez-Vázquez
Antibiotics 2023, 12(6), 1010; https://doi.org/10.3390/antibiotics12061010 - 5 Jun 2023
Cited by 2 | Viewed by 1608
Abstract
Extended-spectrum β-lactamase (ESBL)-producing E. coli has become an important global problem for the public health sector. This study aims to investigate the E. coli antimicrobial resistance profile among living food-producing animals in Tamaulipas, Mexico. A total of 200 fecal samples were collected from [...] Read more.
Extended-spectrum β-lactamase (ESBL)-producing E. coli has become an important global problem for the public health sector. This study aims to investigate the E. coli antimicrobial resistance profile among living food-producing animals in Tamaulipas, Mexico. A total of 200 fecal samples were collected from bovines, pigs, chickens and sheep. A total of 5.0% of the strains were phenotypically confirmed as ESBL producers. A high percentage of phenotypic antimicrobial resistance was observed against gentamicin (93.3%), tetracycline (86.6%) and streptomycin (83.3%). The gentamicin-resistant strains showed MDR, distributed among 27 resistance patterns to different antimicrobials. The antimicrobial resistance gene tet(A) was detected in 73.3% of isolates, aadA1 in 60.0% and sul2 in 43.3% of strains. The blaCTX-M gene was found in 23.3% of strains. The virulence gene hlyA was detected in 43.3% of isolates; stx1 and stx2 were not detected in any strain. The phylotyping indicated that the isolates belonged to groups A (33.3%), B1 (16.6%), B2 (40.0%) and D (10.0%). These results show that food-producing animals might be a reservoir of ESBL-producing bacteria and may play a role in their spread. Full article
Show Figures

Figure 1

11 pages, 306 KiB  
Article
Antimicrobial Usage and Detection of Multidrug-Resistant Staphylococcus aureus: Methicillin- and Tetracycline-Resistant Strains in Raw Milk of Lactating Dairy Cattle
by Lubna, Tahir Hussain, Ashwag Shami, Naseem Rafiq, Shehryar Khan, Muhammad Kabir, Naimat Ullah Khan, Irfan Khattak, Mustafa Kamal and Tahir Usman
Antibiotics 2023, 12(4), 673; https://doi.org/10.3390/antibiotics12040673 - 29 Mar 2023
Cited by 5 | Viewed by 2386
Abstract
Staphylococcus aureus is a prominent cause of food-borne diseases worldwide. Enterotoxigenic strains of this bacteria are frequently found in raw milk, and some of these strains are resistant to antimicrobials, posing a risk to consumers. The main objectives of this study were to [...] Read more.
Staphylococcus aureus is a prominent cause of food-borne diseases worldwide. Enterotoxigenic strains of this bacteria are frequently found in raw milk, and some of these strains are resistant to antimicrobials, posing a risk to consumers. The main objectives of this study were to determine the antimicrobial resistance pattern of S. aureus in raw milk and to detect the presence of mecA and tetK genes in it. A total of 150 milk samples were obtained aseptically from lactating cattle, including Holstein Friesian, Achai, and Jersey breeds, maintained at different dairy farms. The milk samples were checked for the presence of S. aureus, and it was detected in 55 (37%) of them. The presence of S. aureus was verified by culturing on selective media, gram staining, and performing coagulase and catalase tests. Further confirmation was performed through PCR with a species-specific thermonuclease (nuc) gene. Antimicrobial susceptibility testing of the confirmed S. aureus was then determined by using the Kirby–Bauer disc diffusion technique. Out of the 55 confirmed S. aureus isolates, 11 were determined to be multidrug-resistant (MDR). The highest resistance was found to penicillin (100%) and oxacillin (100%), followed by tetracycline (72.72%), amikacin (27.27%), sulfamethoxazole/trimethoprim (18.18%), tobramycin (18.18%), and gentamycin (9.09%). Amoxicillin and ciprofloxacin were found to be susceptible (100%). Out of 11 MDR S. aureus isolates, the methicillin resistance gene (mecA) was detected in 9 isolates, while the tetracycline resistance gene (tetK) was found in 7 isolates. The presence of these methicillin- and tetracycline-resistant strains in raw milk poses a major risk to public health, as they can cause food poisoning outbreaks that can spread rapidly through populations. Our study concludes that out of nine empirically used antibiotics, amoxicillin, ciprofloxacin, and gentamicin were highly effective against S. aureus compared to penicillin, oxacillin, and tetracycline. Full article
12 pages, 1849 KiB  
Article
Phenotypic and Genotypic Investigation of Carbapenem-Resistant Acinetobacter baumannii in Maharaj Nakhon Si Thammarat Hospital, Thailand
by Sirijan Santajit, Phuangthip Bhoopong, Thida Kong-Ngoen, Witawat Tunyong, Dararat Horpet, Wanfudhla Paehoh-ele, Tasneem Zahedeng, Pornpan Pumirat, Nitat Sookrung, Woranich Hinthong and Nitaya Indrawattana
Antibiotics 2023, 12(3), 580; https://doi.org/10.3390/antibiotics12030580 - 15 Mar 2023
Cited by 2 | Viewed by 2880
Abstract
(1) Background: Acinetobacter baumannii is well known as a causative agent of severe hospital-acquired infections, especially in intensive care units. The present study characterised the genetic traits of biofilm-forming carbapenem-resistant A. baumannii (CRAB) clinical isolates. Additionally, this study determined the prevalence of biofilm-producing [...] Read more.
(1) Background: Acinetobacter baumannii is well known as a causative agent of severe hospital-acquired infections, especially in intensive care units. The present study characterised the genetic traits of biofilm-forming carbapenem-resistant A. baumannii (CRAB) clinical isolates. Additionally, this study determined the prevalence of biofilm-producing A. baumannii isolates from a tertiary care hospital and investigated the association of biofilms with the distribution of biofilm-related and antibiotic resistance-associated genotypes. (2) Methods: The 995 non-duplicate A. baumannii isolates were identified, and their susceptibilities to different antibiotics were determined using the disk diffusion method. Using the modified microtiter plate assay, the CRAB isolates were investigated for their biofilm formation ability. Hemolysin and protease activities were determined. CRABs were subjected to polymerase chain reaction (PCR) assays targeting blaVIM, blaNDM, blaIMP, blaOXA-23-like, blaOXA-24-like, blaOXA-51-like, csuE and pgaB genes. Individual CRAB isolates were identified for their DNA fingerprint by repetitive element sequence-based (REP)-PCR. (3) Results: Among all A. baumannii isolates, 172 CRABs were identified. The major antibiotic resistance gene among the CRAB isolates was blaOXA-51-like (100%). Ninety-nine isolates (57.56%) were biofilm producers. The most prevalent biofilm gene was pgaB (79.65%), followed by csuE (76.74%). Evidence of virulence phenotypes revealed that all CRAB exhibited proteolytic activity; however, only four isolates (2.33%) were positive for the hemolytic-producing phenotype. REP-PCR showed that 172 CRAB isolates can be divided into 36-DNA fingerprint patterns. (4) Conclusions: The predominance of biofilm-producing CRAB isolates identified in this study is concerning. The characterisation of risk factors could aid in controlling the continual selection and spreading of the A. baumannii phenotype in hospitals, thereby improving patient care quality. Full article
Show Figures

Figure 1

18 pages, 815 KiB  
Article
Estimation, Evaluation and Characterization of Carbapenem Resistance Burden from a Tertiary Care Hospital, Pakistan
by Aamir Jamal Gondal, Nakhshab Choudhry, Hina Bukhari, Zainab Rizvi, Shah Jahan and Nighat Yasmin
Antibiotics 2023, 12(3), 525; https://doi.org/10.3390/antibiotics12030525 - 6 Mar 2023
Cited by 5 | Viewed by 2918
Abstract
Carbapenem resistance has become major concern in healthcare settings globally; therefore, its monitoring is crucial for intervention efforts to halt resistance spread. During May 2019–April 2022, 2170 clinical strains were characterized for antimicrobial susceptibility, resistance genes, replicon and sequence types. Overall, 42.1% isolates [...] Read more.
Carbapenem resistance has become major concern in healthcare settings globally; therefore, its monitoring is crucial for intervention efforts to halt resistance spread. During May 2019–April 2022, 2170 clinical strains were characterized for antimicrobial susceptibility, resistance genes, replicon and sequence types. Overall, 42.1% isolates were carbapenem-resistant, and significantly associated with Klebsiella pneumoniae (K. pneumoniae) (p = 0.008) and Proteus species (p = 0.043). Carbapenemases were detected in 82.2% of isolates, with blaNDM-1 (41.1%) associated with the ICU (p < 0.001), cardiology (p = 0.042), pediatric medicine (p = 0.013) and wound samples (p = 0.041); blaOXA-48 (32.6%) was associated with the ICU (p < 0.001), cardiology (p = 0.008), pediatric medicine (p < 0.001), general surgery (p = 0.001), general medicine (p = 0.005) and nephrology (p = 0.020); blaKPC-2 (5.5%) was associated with general surgery (p = 0.029); blaNDM-1/blaOXA-48 (11.4%) was associated with general surgery (p < 0.001), and wound (p = 0.002), urine (p = 0.003) and blood (p = 0.012) samples; blaOXA-48/blaVIM (3.1%) was associated with nephrology (p < 0.001) and urine samples (p < 0.001). Other detected carbapenemases were blaVIM (3.0%), blaIMP (2.7%), blaOXA-48/blaIMP (0.1%) and blaVIM/blaIMP (0.3%). Sequence type (ST)147 (39.7%) represented the most common sequence type identified among K. pneumoniae, along with ST11 (23.0%), ST14 (15.4%), ST258 (10.9%) and ST340 (9.6%) while ST405 comprised 34.5% of Escherichia coli (E. coli) isolates followed by ST131 (21.2%), ST101 (19.7%), ST10 (16.0%) and ST69 (7.4%). Plasmid replicon types IncFII, IncA/C, IncN, IncL/M, IncFIIA and IncFIIK were observed. This is first report describing the carbapenem-resistance burden and emergence of blaKPC-2-ST147, blaNDM-1-ST340 and blaNDM-1-ST14 in K. pneumoniae isolates and blaNDM-1-ST69 and blaNDM-1/blaOXA-48-ST69 in E. coli isolates coharboring extended-spectrum beta-lactamases (ESBLs) from Pakistan. Full article
Show Figures

Figure 1

10 pages, 291 KiB  
Article
Molecular and Antimicrobial Susceptibility Characterization of Escherichia coli Isolates from Bovine Slaughterhouse Process
by José Vázquez-Villanueva, Karina Vázquez, Ana Verónica Martínez-Vázquez, Alfredo Wong-González, Jesus Hernández-Escareño, Omar Cabrero-Martínez, Wendy Lizeth Cruz-Pulido, Abraham Guerrero, Gildardo Rivera and Virgilio Bocanegra-García
Antibiotics 2023, 12(2), 291; https://doi.org/10.3390/antibiotics12020291 - 1 Feb 2023
Cited by 3 | Viewed by 1938
Abstract
Antimicrobials are routinely used in human and veterinary medicine. With repeated exposure, antimicrobials promote antibiotic resistance, which poses a threat to public health. In this study, we aimed to determine the susceptibility patterns, virulence factors, and phylogroups of E. coli isolates during the [...] Read more.
Antimicrobials are routinely used in human and veterinary medicine. With repeated exposure, antimicrobials promote antibiotic resistance, which poses a threat to public health. In this study, we aimed to determine the susceptibility patterns, virulence factors, and phylogroups of E. coli isolates during the killing process in a bovine slaughterhouse. We analyzed 336 samples (from water, surfaces, carcasses, and feces), and 83.3% (280/336) were positive for E. coli. The most common phenotypic resistances that we detected were 50.7% (142/280) for tetracycline, 44.2% (124/280) for cephalothin, 34.6% (97/280) for streptomycin, and 36.7% (103/280) for ampicillin. A total of 82.4% of the isolates had resistance for at least one antimicrobial, and 37.5% presented multiresistance. We detected a total of 69 different phenotypic resistance patterns. We detected six other resistance-related genes, the most prevalent being tetA (22.5%) and strB (15.7%). The prevalence values of the virulence genes were 5.4% in hlyA, 1.4% in stx1, and 0.7% in stx2. The frequencies of the pathogenic strains (B2 and D) were 32.8% (92/280) and 67.1% (188/280) as commensals A and B1, respectively. E. coli isolates with pathogenic potential and multiresistance may represent an important source of dissemination and a risk to consumers. Full article
16 pages, 3897 KiB  
Article
High-Throughput Transcriptomic Profiling Reveals the Inhibitory Effect of Hydroquinine on Virulence Factors in Pseudomonas aeruginosa
by Nontaporn Rattanachak, Sattaporn Weawsiangsang, Krai Daowtak, Yordhathai Thongsri, Sukunya Ross, Gareth Ross, Nungruthai Nilsri, Robert A. Baldock, Sutatip Pongcharoen, Touchkanin Jongjitvimol and Jirapas Jongjitwimol
Antibiotics 2022, 11(10), 1436; https://doi.org/10.3390/antibiotics11101436 - 19 Oct 2022
Cited by 3 | Viewed by 4392
Abstract
Hydroquinine is an organic alkaloid compound that exhibits antimicrobial activity against several bacterial strains including strains of both drug-sensitive and multidrug-resistant P. aeruginosa. Despite this, the effects of hydroquinine on virulence factors in P. aeruginosa have not yet been characterized. We [...] Read more.
Hydroquinine is an organic alkaloid compound that exhibits antimicrobial activity against several bacterial strains including strains of both drug-sensitive and multidrug-resistant P. aeruginosa. Despite this, the effects of hydroquinine on virulence factors in P. aeruginosa have not yet been characterized. We therefore aimed to uncover the mechanism of P. aeruginosa hydroquinine-sensitivity using high-throughput transcriptomic analysis. We further confirmed whether hydroquinine inhibits specific virulence factors using RT-qPCR and phenotypic analysis. At half the minimum inhibitory concentration (MIC) of hydroquinine (1.250 mg/mL), 254 genes were differentially expressed (97 downregulated and 157 upregulated). We found that flagellar-related genes were downregulated by between −2.93 and −2.18 Log2-fold change. These genes were consistent with the analysis of gene ontology and KEGG pathway. Further validation by RT-qPCR showed that hydroquinine significantly suppressed expression of the flagellar-related genes. By analyzing cellular phenotypes, P. aeruginosa treated with ½MIC of hydroquinine exhibited inhibition of motility (30–54% reduction) and pyocyanin production (~25–27% reduction) and impaired biofilm formation (~57–87% reduction). These findings suggest that hydroquinine possesses anti-virulence factors, through diminishing flagellar, pyocyanin and biofilm formation. Full article
Show Figures

Figure 1

Back to TopTop