How should we respond to the emergence of plasmid-mediated colistin resistance in humans and animals?

Prevalence of Antimicrobial Resistance in Escherichia coli and Salmonella Species Isolates from Chickens in Live Bird Markets and Boot Swabs from Layer Farms in Timor-Leste

The rapid emergence of antimicrobial resistance is a global concern, and high levels of resistance have been detected in chicken populations worldwide. The purpose of this study was to determine the prevalence of antimicrobial resistance in Escherichia coli and Salmonella spp. isolated from healthy chickens in Timor-Leste. Through a cross-sectional study, cloacal swabs and boot swabs were collected from 25 live bird markets and two layer farms respectively. E. coli and Salmonella spp. from these samples were tested for susceptibility to six antimicrobials using a disk diffusion test, and a subset was tested for susceptibility to 27 antimicrobials using broth-based microdilution. E. coli and Salmonella spp. isolates showed the highest resistance towards either tetracycline or ampicillin on the disk diffusion test. E. coli from layer farms (odds ratio:5.2; 95%CI 2.0-13.1) and broilers (odds ratio:18.1; 95%CI 5.3-61.2) were more likely to be multi-drug resistant than those from local chickens. Based on the broth-based microdilution test, resistance to antimicrobials in the Timor-Leste Antimicrobial Guidelines for humans were low, except for resistance to ciprofloxacin in Salmonella spp. (47.1%). Colistin resistance in E. coli was 6.6%. Although this study shows that antimicrobial resistance in chickens was generally low in Timor-Leste, there should be ongoing monitoring in commercial chickens as industry growth might be accompanied with increased antimicrobial use.

Isolation of Carbapenem and Colistin Resistant Gram-Negative Bacteria Colonizing Immunocompromised SARS-CoV-2 Patients Admitted to Some Libyan Hospitals

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a devastating effect, globally. We describe, for the first time, the occurrence of carbapenem-resistant bacteria colonizing SARS-CoV-2 patients who developed hospital-associated infections with carbapenemase-producing, Gram-negative bacteria at some isolation centers of SARS-CoV-2 in the eastern part of Libya. In total, at first, 109 samples were collected from 43 patients, with the samples being recovered from oral (n = 35), nasal (n = 45), and rectal (n = 29) cavities. Strain identification was performed via matrix assisted laser desorption ionization-time of flight (MALDI-TOF). Antibiotic susceptibility testing was carried out on Mueller-Hinton agar, using the standard disk diffusion method. MIC determination was confirmed via E-TEST and microdilution standard methods. A molecular study was carried out to characterize the carbapenem and colistin resistance in Gram-negative bacterial strains. All of the positive results were confirmed via sequencing. Klebsiella pneumoniae (n = 32), Citrobacter freundii (n = 21), Escherichia coli (n = 7), and Acinetobacter baumannii (n = 21) were the predominant isolated bacteria. Gram-negative isolates were multidrug-resistant and carried different carbapenem resistance-associated genes, including NDM-1 (56/119; 47.05%), OXA-48 (15/119; 12.60%), OXA-23 (19/119; 15.96%), VIM (10/119; 8.40%), and the colistin resistance mobile gene mcr-1 (4/119; 3.36%). The overuse of antimicrobials, particularly carbapenem antibiotics, during the SARS-CoV-2 pandemic has led to the emergence of multidrug-resistant bacteria, mainly K. pneumoniae, A. baumannii, and colistin-resistant E. coli strains. Increased surveillance as well as the rational use of carbapenem antibiotics and, recently, colistin are required to reduce the propagation of multidrug-resistant strains and to optimally maintain the efficacy of these antibiotics. IMPORTANCE In this work, we describe, for the first time, the occurrence of carbapenem-resistant bacteria colonizing COVID-19 patients who developed hospital-associated infections with carbapenemase-producing, Gram-negative bacteria at some isolation centers of COVID-19 in the eastern part of Libya. Our results confirmed that the overuse of antimicrobials, such as carbapenem antibiotics, during the COVID-19 pandemic has led to the emergence of multidrug-resistant bacteria, mainly K. pneumoniae and A. baumannii, as well as colistin resistance.

Polymyxin combination therapy for multidrug-resistant, extensively-drug resistant, and difficult-to-treat drug-resistant gram-negative infections: is it superior to polymyxin monotherapy?

INTRODUCTION

The increasing prevalence of infections with multidrug-resistant (MDR), extensively-drug resistant (XDR) or difficult-to-treat drug resistant (DTR) Gram-negative bacilli (GNB), including Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, Enterobacter species, and Escherichia coli poses a severe challenge.

AREAS COVERED

The rapid growing of multi-resistant GNB as well as the considerable deceleration in development of new anti-infective agents have made polymyxins (e.g. polymyxin B and colistin) a mainstay in clinical practices as either monotherapy or combination therapy. However, whether the polymyxin-based combinations lead to better outcomes remains unknown. This review mainly focuses on the effect of polymyxin combination therapy versus monotherapy on treating GNB-related infections. We also provide several factors in designing studies and their impact on optimizing polymyxin combinations.

EXPERT OPINION

An abundance of recent in vitro and preclinical in vivo data suggest clinical benefit for polymyxin-drug combination therapies, especially colistin plus meropenem and colistin plus rifampicin, with synergistic killing against MDR, XDR, and DTR P. aeruginosa, K. pneumoniae and A. baumannii. The beneficial effects of polymyxin-drug combinations (e.g. colistin or polymyxin B + carbapenem against carbapenem-resistant K. pneumoniae and carbapenem-resistant A. baumannii, polymyxin B + carbapenem + rifampin against carbapenem-resistant K. pneumoniae, and colistin + ceftolozan/tazobactam + rifampin against PDR-P. aeruginosa) have often been shown in clinical setting by retrospective studies. However, high-certainty evidence from large randomized controlled trials is necessary. These clinical trials should incorporate careful attention to patient's sample size, characteristics of patient's groups, PK/PD relationships and dosing, rapid detection of resistance, MIC determinations, and therapeutic drug monitoring.

Rapid culture-independent loop-mediated isothermal amplification detection of antimicrobial resistance markers from environmental water samples

Environmental water is considered one of the main vehicles for the transmission of antimicrobial resistance (AMR), posing an increasing threat to humans and animals health. Continuous efforts are being made to eliminate AMR; however, the detection of AMR pathogens from water samples often requires at least one culture step, which is time-consuming and can limit sensitivity. In this study, we employed comparative genomics to identify the prevalence of AMR genes within among: Escherichia coli, Klebsiella, Salmonella enterica and Acinetobacter, using publicly available genomes. The mcr-1, blaKPC (KPC-1 to KPC-4 alleles), blaOXA-48, blaOXA-23 and blaVIM (VIM-1 and VIM-2 alleles) genes are of great medical and veterinary significance, thus were selected as targets for the development of isothermal loop-mediated amplification (LAMP) detection assays. We also developed a rapid and sensitive sample preparation method for an integrated culture-independent LAMP-based detection from water samples. The developed assays successfully detected the five AMR gene markers from pond water within 1 h and were 100% sensitive and specific with a detection limit of 0.0625 μg/mL and 10 cfu/mL for genomic DNA and spiked bacterial cells, respectively. The integrated detection can be easily implemented in resource-limited areas to enhance One Health AMR surveillances and improve diagnostics.

Metagenomic insights into the antibiotic resistomes of typical Chinese dairy farm environments

Antibiotic resistance genes (ARGs) in the environment pose a threat to human and animal health. Dairy cows are important livestock in China; however, a comprehensive understanding of antibiotic resistance in their production environment has not been well clarified. In this study, we used metagenomic methods to analyze the resistomes, microbiomes, and potential ARG bacterial hosts in typical dairy farm environments (including feces, wastewater, and soil). The ARGs resistant to tetracyclines, MLS, β-lactams, aminoglycoside, and multidrug was dominant in the dairy farm ecosystem. The abundance and diversity of total ARGs in dairy feces and wastewater were significantly higher than in soil (P < 0.05). The same environmental samples from different dairy have similar resistomes and microbiomes. A high detection rate of tet(X) in wastewater and feces (100% and 71.4%, respectively), high abundance (range from 5.74 to 68.99 copies/Gb), and the finding of tet(X5) challenged the clinical application of the last antibiotics resort of tigecycline. Network analysis identified Bacteroides as the dominant genus in feces and wastewater, which harbored the greatest abundance of their respective total ARG coverage and shared ARGs. These results improved our understanding of ARG profiles and their bacterial hosts in dairy farm environments and provided a basis for further surveillance.

Molecular mechanisms and clonal lineages of colistin-resistant bacteria across the African continent: A scoping review

Colistin (also known as Polymyxin E), a polymyxin antibiotic discovered in the late 1940s, has recently reemerged as a last-line treatment option for multidrug-resistant infections. However, in recent years, colistin-resistant pathogenic bacteria have been increasingly reported worldwide. Accordingly, the presented review was undertaken to identify, integrate and synthesize current information regarding the detection and transmission of colistin-resistant bacteria across the African continent, in addition to elucidating their molecular mechanisms of resistance. PubMed, Google Scholar, and Science Direct were employed for study identification, screening and extraction. Overall, based on the developed literature review protocol and associated inclusion/exclusion criteria, 80 studies published between 2000 and 2021 were included comprising varying bacterial species and hosts. Numerous mechanisms of colistin resistance were reported, including chromosomal mutation(s) and transferable plasmid-mediated colistin resistance (encoded by mcr genes). Perhaps unexpectedly, mcr-variants have exhibited rapid emergence and spread across most African regions. The genetic variant mcr-1 is predominant in humans, animals, and the natural environment, and is primarily carried by IncHI2- type plasmid. The highest numbers of studies reporting the dissemination of colistin-resistant Gram-negative bacteria were conducted in the North African region.

Carbapenemase Production and Detection of Colistin-Resistant Genes in Clinical Isolates of Escherichia Coli from the Ho Teaching Hospital, Ghana

Background

Effective and successful treatment of infectious diseases is a significant gain in clinical settings. However, resistance to antibiotics, especially the last-resort medicines, including carbapenems and colistin is on the rise.

Aim

The aim of this study was to detect carbapenemase production and colistin-resistant genes in clinical isolates of Escherichia coli. Method. The study was a cross-sectional study carried out from July 2018 to June 2019. One hundred and thirty-five nonrepetitive E. coli isolates obtained from various clinical samples were screened for carbapenemase production using meropenem (10 μg) and imipenem (10 μg) disks. Screened-positive isolates were further subjected to a confirmatory test using modified carbapenem inhibition method (mCIM). Deoxyribonucleic acid (DNA) was extracted from all the isolates to detect colistin-resistant genes by polymerase chain reaction. Data were analyzed using GraphPad Prism version 8.00 for Windows and IBM SPSS version 26 (IMB Corp. New York, USA).

Results

Of the 135 isolates, 2 were screened positive for carbapenemase production but tested negative to mCIM. With the colistin-resistant genes, only mcr-1 and mcr-2_700bp were detected in 3 of the E. coli isolates, representing 2.2%. The mcr-1 was detected in a high vaginal swab sample of a female aged between 65 and 84 years. Mcr-2_700bp was also detected in urine and blood samples of the patients.

Conclusion

The study investigated the presence of carbapenemase and colistin-resistant genes in E. coli organisms. The absence of carbapenemase in the isolates and the detection of colistin-genes call for strict infection prevention and control practices to prevent their introduction and spread to other bacterial species, respectively.

Mobile Colistin Resistance (mcr) Genes in Cats and Dogs and Their Zoonotic Transmission Risks

Background: Pets, especially cats and dogs, represent a great potential for zoonotic transmission, leading to major health problems. The purpose of this systematic review was to present the latest developments concerning colistin resistance through mcr genes in pets. The current study also highlights the health risks of the transmission of colistin resistance between pets and humans. Methods: We conducted a systematic review on mcr-positive bacteria in pets and studies reporting their zoonotic transmission to humans. Bibliographic research queries were performed on the following databases: Google Scholar, PubMed, Scopus, Microsoft Academic, and Web of Science. Articles of interest were selected using the PRISMA guideline principles. Results: The analyzed articles from the investigated databases described the presence of mcr gene variants in pets including mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, mcr-8, mcr-9, and mcr-10. Among these articles, four studies reported potential zoonotic transmission of mcr genes between pets and humans. The epidemiological analysis revealed that dogs and cats can be colonized by mcr genes that are beginning to spread in different countries worldwide. Overall, reported articles on this subject highlight the high risk of zoonotic transmission of colistin resistance genes between pets and their owners. Conclusions: This review demonstrated the spread of mcr genes in pets and their transmission to humans, indicating the need for further measures to control this significant threat to public health. Therefore, we suggest here some strategies against this threat such as avoiding zoonotic transmission.

Worldwide Prevalence of mcr-mediated Colistin-Resistance Escherichia coli in Isolates of Clinical Samples, Healthy Humans, and Livestock-A Systematic Review and Meta-Analysis

Background: Antimicrobial resistance is a serious public-health problem throughout the world. Escherichia coli, the most common Gram-negative microorganism, has developed different resistance mechanisms, making treating infections difficult. Colistin is considered a last-resort drug in the treatment of infections caused by E. coli. Plasmid-mediated mobile-colistin-resistant (mcr) genes in E. coli, now disseminated globally, are considered a major public-health threat. Humans, chickens, and pigs are the main reservoirs for E. coli and the sources of antibiotic resistance. Hence, an up-to-date and precise estimate of the global prevalence of mcr resistance genes in these reservoirs is necessary to understand more precisely the worldwide spread and to more effectively implement control and prevention strategies. Methodology: Publications were identified in the PubMed database on the basis of the PRISMA guidelines. English full-text articles were selected from December 2014 to March 2021. Descriptive statistics and a meta-analysis were performed in Excel and R software, respectively. Colistin resistance was defined as the molecular-genetic detection of the mcr genes. The crude and estimated prevalence were calculated for each host and continent. The studies were divided into two groups; community-based when they involved isolates from healthy humans, chickens, or pigs, and clinical studies when they involved only hospital, outpatient, or laboratory isolates. Results: A total of 1278 studies were identified and 218 were included in this systematic review and meta-analysis, divided into community studies (159 studies) and clinical studies (59 studies). The general prevalence of mcr-mediated colistin-resistant E. coli (mcrMCRE) was 6.51% (n = 11,583/177,720), reported in 54 countries and on five continents; Asia with 119 studies followed by Europe with 61 studies registered the most articles. Asia reported the major diversity of mcr-variants (eight of nine, except mcr-2). Worldwide, chickens and pigs proved to be the principal reservoir of mcr with an estimated prevalence of 15.8% and 14.9%, respectively. Healthy humans and clinical isolates showed a lower prevalence with 7.4% and 4.2% respectively. Conclusions: In this systematic review and meta-analysis, the worldwide prevalence of mcr in E. coli isolated from healthy humans, chickens, and pigs was investigated. A wide prevalence and distribution of mcr genes was demonstrated on all continents in E. coli isolates from the selected reservoirs. Understanding the epidemiology and occurrence in the reservoirs of mcr in E. coli on different continents of the world facilitates tracing how mcr genes are transmitted and determining the infection risks for humans. This knowledge can be used to reduce the incidence of zoonotic transmission by implementing the appropriate control programs.

Methodology for laboratory-based antimicrobial resistance surveillance in animals

Antimicrobial resistance (AMR) is a crucial and emerging multifactorial “One Health” problem involving human and animal health, agriculture, aquaculture, and environment; and posing a potential public health hazard globally. The containment of AMR justifies effective surveillance programs to explicate the magnitude of the problem across the contributing sectors. Laboratory-based AMR testing and characterization is the key component of an AMR surveillance program. An AMR surveillance program should have a “top management” for fund mobilization, planning, formulating, and multilateral coordinating of the surveillance activities. The top management should identify competent participating laboratories to form a network comprising a reference laboratory and an adequate number of sentinel laboratories. The responsibilities of the reference laboratory include the development of standardized test methods for ensuring quality and homogeneity of surveillance activities, providing training to the laboratory personnel, and in-depth AMR characterization. The sentinel laboratories will take the responsibilities of receiving samples, isolation and identification of microbes, and initial AMR characterization. The sentinel laboratories will use simple antimicrobial susceptibility test (AST) methods such as disk diffusion tests, whereas the reference laboratories should use automated quantitative AST methods as well as advanced molecular methods to explicit AMR emergence mechanisms. Standard guidelines set by Clinical Laboratory Standards Institute or the European Committee on Antimicrobial Susceptibility Testing, should be followed to bring about conformity and harmonization in the AST procedures. AMR surveillance program in animals is eventually similar to that in human health with the exception is that veterinary antibiotics and veterinary pathogens should be given preference here. Hence, the review study was envisaged to look deep into the structure of the AMR surveillance program with significance on laboratory-based AMR testing and characterization methods.

Re-sensitization of mcr carrying multidrug resistant bacteria to colistin by silver

Superbugs carrying a mobile colistin resistance gene (mcr) are jeopardizing the clinical efficacy of the last-line antibiotic colistin. The development of MCR inhibitors is urgently required to cope with antibiotic-resistance emergencies. Here, we show that silver (Ag⁺) fully restores the susceptibility of mcr-1–carrying superbugs against colistin both in vitro and in vivo. We found an unprecedented tetra-silver center in the active-site pocket of MCR-1 through the substitution of the essential Zn²⁺ ions in the intact enzyme, leading to the prevention of substrate binding (i.e. the dysfunction of MCR-1 in transferring phosphorylethanolamine to lipid A). Importantly, the ability of Ag⁺ to suppress resistance evolution extends the lifespan of currently used antibiotics, providing a strategy to treat infections by mcr-positive bacteria.

Colistin is considered the last-line antimicrobial for the treatment of multidrug-resistant gram-negative bacterial infections. The emergence and spread of superbugs carrying the mobile colistin resistance gene (mcr) have become the most serious and urgent threat to healthcare. Here, we discover that silver (Ag⁺), including silver nanoparticles, could restore colistin efficacy against mcr-positive bacteria. We show that Ag⁺ inhibits the activity of the MCR-1 enzyme via substitution of Zn²⁺ in the active site. Unexpectedly, a tetra-silver center was found in the active-site pocket of MCR-1 as revealed by the X-ray structure of the Ag-bound MCR-1, resulting in the prevention of substrate binding. Moreover, Ag⁺ effectively slows down the development of higher-level resistance and reduces mutation frequency. Importantly, the combined use of Ag⁺ at a low concentration with colistin could relieve dermonecrotic lesions and reduce the bacterial load of mice infected with mcr-1–carrying pathogens. This study depicts a mechanism of Ag⁺ inhibition of MCR enzymes and demonstrates the potentials of Ag⁺ as broad-spectrum inhibitors for the treatment of mcr-positive bacterial infection in combination with colistin.

Mechanisms underlying the effect of chlorination and UV disinfection on VBNC state Escherichia coli isolated from hospital wastewater

The occurrence of viable but non-culturable (VBNC) bacteria in the wastewater system poses a huge threat to environmental and public health, in particular in hospital wastewater treatment system (HWTS). HWTS-oriented studies have been conducted to assess the effectiveness of chlorination and UV disinfection using indigenous bacteria. Results revealed that the VBNC Escherichia coli and ARGs remained persistent even at high chlorination (12 mg/L for 2.5 h) and UV doses (1000 mJ/cm²). The molecular mechanisms underlying chlorination-/UV-induced VBNC state in E. coli were explored through the transcriptomics and results suggested that most energy-dependent physiological activities (e.g., metabolism) have been suppressed in VBNC E. coli, while the pathogenicity-related genes varied insignificantly compared to the culturable cells, indicating that the VBNC E. coli could potentially display pathogenicity. Further Galleria mellonella model experiment has confirmed that although the disinfection-induced VBNC state made cells less infectious, these cells could regain their pathogenicity after resuscitation. This in vitro study can be used as a reference for studies on infections from VBNC bacteria and highlights the health risk due to VBNC pathogens in hospital effluents. There is a need to develop effluent standards specifically for healthcare facilities, and a stricter downstream disinfection strategy should be considered for the removal of VBNC cells and ARGs in the effluent.

Characterization of the genetic structure of mcr-1 gene among Escherichia coli isolates recovered from surface waters and sediments from Ecuador

Although anthropogenic activities contribute to the selection and spread of antibiotic resistance in aquatic environments, limited information is available from countries with absent or incomplete sewage treatment systems and the impact of their discharges onto water bodies. This study therefore aimed to characterize the genetic structure of colistin resistance (mcr) genes among Escherichia coli isolates recovered from surface waters and sediments in Ecuador. Out of 459 isolates, four Escherichia coli showed multidrug-resistant phenotypes, which harbored the mcr-1 gene and β-lactamases, such as bla_TEM, bla_CTX-M-15, bla_CTX-M-55, or bla_CTX-M-65 genes. Three E. coli isolates (U20, U30 and U144) shared a similar genetic environment surrounding the mcr-1 gene, which was located on plasmids. Only one E. coli isolate (U175) showed that the mcr-1 gene was chromosomally located. Moreover, the core genome multilocus sequence typing (cgMLST) analysis revealed that these isolates belong to different lineages. This study represents the first detection of the mcr-1 gene in multidrug-resistant E. coli isolates from environmental samples in Ecuador.

Overview of polymyxin resistance in Enterobacteriaceae

Polymyxin antibiotics are disfavored owing to their potential clinical toxicity, especially nephrotoxicity. However, the dry antibiotic development pipeline, together with the increasing global prevalence of infections caused by multidrug-resistant (MDR) gram-negative bacteria, have renewed clinical interest in these polypeptide antibiotics. This review highlights the current information regarding the mechanisms of resistance to polymyxins and their molecular epidemiology. Knowledge of the resistance mechanisms and epidemiology of these pathogens is critical for the development of novel antibacterial agents and rapid treatment choices.

Opportunities to enhance antibiotic stewardship: colistin use and outcomes in a low-resource setting

Background

Colistin use is increasing with the rise in MDR Gram-negative infections globally. Effective antibiotic stewardship is essential to preserve this antibiotic of last resort.

Objectives

This study investigated stewardship and safety errors related to colistin use to identify opportunities for improvement.

Patients and methods

A prospective descriptive study involving all patients 13 years and older treated with colistin at a tertiary hospital in Cape Town, South Africa, between August 2018 and June 2019. We collected clinical, laboratory and outcome data and assessed provided treatment for stewardship and safety errors.

Results

We included 44 patients. Treatment errors were identified for 34 (77%) patients (median = 1), most commonly inadequate monitoring of renal function (N = 16, 32%). We also identified no rational indication for colistin (N = 9, 20%), loading dose error (N = 12, 27%); maintenance dose error (N = 10, 23%); no prior culture (N = 11, 25%); and failure to de-escalate (2 of 9) or adjust dose to changes in renal function (6 of 15). All cause in-hospital mortality was 47%. Amongst survivors, median ICU stay was 6 days and hospital stay more than 30 days. Eight (18%) patients developed renal injury or failure during treatment. Three (7%) patients in this study were found to have colistin-resistant organisms including two prior to colistin exposure.

Conclusions

This study has identified opportunities to enhance colistin stewardship and improve efficacy and safety of prescription. The appearance of colistin-resistant organisms reinforces the urgent need to ensure effective and appropriate use of colistin.

Distribution of antibiotic resistance genes in the environment

The prevalence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the microbiome is a major public health concern globally. Many habitats in the environment are under threat due to excessive use of antibiotics and evolutionary changes occurring in the resistome. ARB and ARGs from farms, cities and hospitals, wastewater treatment plants (WWTPs) or as water runoffs, may accumulate in water, soil, and air. We present a global picture of the resistome by examining ARG-related papers retrieved from PubMed and published in the last 30 years (1990-2020). Natural Language Processing (NLP) was used to retrieve 496,640 papers, out of which 9374 passed the filtering test and were further analyzed to determine the distribution and diversity of ARG subtypes. The papers revealed seven major antibiotic families together with their respective ARG subtypes in different habitats on six continents. Asia, especially China, had the highest number of ARGs related papers compared to other countries/regions/continents. ARGs belonging to multidrug, glycopeptide, and β-lactam families were the most common in reports from hospitals and sulfonamide and tetracycline families were common in reports from farms, WWTPs, water and soil. We also highlight the 'omics' tools used in resistome research, describe some factors that shape the development of resistome, and suggest future work needed to better understand the resistome. The goal was to show the global nature of ARB and ARGs in order to encourage collaborate research efforts aimed at reducing the negative impacts of antibiotic resistance on the One Health concept.

A retrospective review of colistin utilisation at a tertiary care academic hospital in South Africa

Background

The use of the antibiotic colistin was increasing as a treatment option for multidrug-resistant (MDR) infections. Standardisation of colistin dosing and more appropriate record-keeping practices were required to fully assess the optimal usage of colistin. The aim of this study was to determine how and why colistin was used in the treatment of MDR infections in a tertiary care public hospital in South Africa (SA).

Methods

This cross-sectional retrospective record review described adult and paediatric patients who received colistin intravenously from 01 May 2016 to 31 April 2017. Information from patient records were captured on a data collection tool and analysed using descriptive statistics. Ethical approval was obtained from the Human Research Ethics Committee of the University of the Witwatersrand.

Results

A total of 43 patient records were reviewed. Acinetobacter baumannii was the most common organism isolated (85.2% adults and 62.5% paediatrics). Colistin was mostly prescribed for sepsis (18 adults and 15 paediatrics). Most adults (66.7%) received loading doses as recommended; however, there was a great variation in maintenance doses. Paediatric patients reviewed also showed varying dosing according to weight. The mean duration of colistin therapy was 10 days. Carbapenems were most commonly co-administered with colistin (58%).

Conclusion

The findings suggested that although colistin usage was restricted in the hospital, it was not adequately monitored or controlled. Doses prescribed were made at the discretion of prescribing doctors and differed to currently accepted guidelines. Improved record-keeping practices related to the monitoring of colistin use were required.

Emergence of IncHI2 Plasmid-Harboring blaNDM-5 from Porcine Escherichia coli Isolates in Guangdong, China

Carbapenem resistance has posed potential harmful risks to human and animals. The objectives of this study were to understand the prevalence of bla_NDM-5 in pigs and investigate the molecular characteristics of NDM-5-producing Escherichia coli isolates in Guangdong province in China. Carbapenem-resistant E. coli isolates were isolated from pigs and obtained using MacConkey plates containing 0.5 mg/L meropenem. Conjugation assay and antimicrobial susceptibility testing were conducted for the isolates and their transconjugants. Whole-genome sequence (WGS) was used to analyze the plasmid genetic feature. A total of five bla_NDM-5-carrying E. coli isolates were obtained in the present investigations. They belonged to five ST types. The bla_NDM-5 genes were found to be in IncX3 and IncHI2 plasmid. The IncX3 plasmid was 46,161 bp in size and identical to other reports. IncHI2 plasmid was 246,593 bp in size and similar to other IncHI2-ST3 plasmids. It consisted of a typical IncHI2 plasmid backbone region and a multiresistance region (MRR). The bla_NDM-5 was closely associated with the IS3000-ISAba125-blaNDM-5-bleMBL-trpF-tat-IS26 unit. We first reported the bla_NDM-5-carrying IncHI2 in E. coli isolates recovered from pigs and revealed the molecular characterization. Continued surveillance for the dissemination of bla_NDM-5 among food-producing animals is required.

Isolation and characterisation of colistin-resistant Enterobacterales from chickens in Southeast Nigeria

OBJECTIVES

Resistance to colistin (CST) mediated by mobile genetic elements has had a broad impact worldwide. There is an intensified call for epidemiological surveillance of mcr in different reservoirs to preserve CST for future generations. In Nigeria, the poultry industry is a key livestock sector. This study was undertaken to screen putative colistin-resistant Enterobacterales (CST-r-E) from poultry birds in Southeast Nigeria and to determine the genetic relatedness of mcr-harbouring isolates.

METHODS

Faecal and cloacal swab samples (n = 785) were collected from chickens in 17 farms located in three contiguous states in Southeast Nigeria between March-November 2018. Following selective culture, CST-r-E were isolated. Confirmation of CST resistance, antimicrobial susceptibility testing, molecular detection of genes mcr-1 to mcr-10, multilocus sequence typing (MLST) and randomly amplified polymorphic DNA (RAPD) analysis were performed on the isolates. A questionnaire was distributed to investigate the knowledge about CST and its use of chicken farm caretakers.

RESULTS

Of the 785 samples evaluated, 45 (5.7%) were positive for 48 CST-r-E, among which 23 harboured the mcr-1 gene (22 Escherichia coli and 1 Klebsiella pneumoniae). In two E.coli isolates, a new allelic variant (mcr-1.22) was detected. RAPD analysis allowed the identification of 11 different fingerprints. MLST also revealed 11 STs, with 3 of them being novel.

CONCLUSION

mcr has significantly spread in poultry birds of Southeast Nigeria, which poses a worrisome risk to veterinary and human health. Strategies to prevent indiscriminate use of CST in farms should be quickly adopted before CST resistance becomes a huge global health issue.

Protected but not from Contamination: Antimicrobial Resistance Profiles of Bacteria from Birds in a Ghanaian Forest Protected Area

Resistance to antimicrobial agents is a growing concern in public health. It has been reported in wildlife from several places in the world though wild animals are not normally exposed to clinically used antimicrobial agents. Despite this, very little research has been done in Ghana to determine antimicrobial resistance in wild animals, particularly those in protected areas. In this study, the presence of colistin resistant and multidrug resistant (MDR) gram-negative bacteria in cloacal swabs of wild birds captured in a Ghanaian forest protected area were evaluated. A total of 195 isolates from 138 individual birds were obtained, identified and tested for resistance to colistin. The colistin-resistant isolates were subsequently tested for multidrug resistance to 4 other antimicrobial agents (Oxytetracycline, Streptomycin, Ampicillin and Ciprofloxacin). Colistin resistance was observed in 6.5% (9/138) of the birds and this was seen in only birds that were sampled close to the reception area of the protected area. About 50% of the colistin-resistant isolates were multidrug resistant. AMR isolates were obtained from birds that have been documented to show an insectivorous or omnivorous feeding preference. Data obtained from the study suggests that AMR and MDR occurred in wild birds from the Conservation Area and supports the claim that proximity to human impacted habitats (settlements/farmlands) increased the likelihood of carriage of AMR. Though the routes of transmission remain unclear, there is potential for spread from the wild birds to other wild/domestic animals and possibly back to humans.

A rapid MALDI-TOF mass spectrometry-based method for colistin susceptibility testing in Escherichia coli

Colistin is recognized as a last‐resort treatment option against multi‐drug resistant bacteria including carbapenem‐resistant Enterobacteriaceae (CRE). However, the plasmid‐mediated colistin‐resistance gene mcr‐1 has been reported globally resulting in an increase of colistin‐resistant bacteria. A quick and accurate method for determining the pathogen resistance of colistin is therefore crucial in the clinic. Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) is a potential tool forto be applied for antimicrobial susceptibility testing. We compared the growth of Escherichia coli strains in the presence or absence of colistin. Automated analyses of the spectra were performed with a prototype software tool written with package R. Three mcr‐1‐positive and six mcr‐1‐negative E. coli were used for establishing the model to obtain the optimal incubation time, the breakpoint concentration of colistin and cut‐off of the relative growth (RG) value. The distinction between susceptible and resistant strains was already noticeable after 2 h of incubation. The best separation between the susceptible and resistant strains was achieved at a concentration of 4 µg ml^‐1 and a relative growth cut‐off value of 0.6. Application of the model for the analysis of 128 E. coli isolates, a sensitivity of 97.4% and a specificity of 88.2% were achieved compared with colistin MIC results. The rapid MALDI‐TOF MS‐based method approach is simple to set‐up, uses a short incubation time, and had excellent outcomes with respect to sensitivity and specificity for colistin sensitivity testing in Escherichia coli.

Combining genetic algorithm with machine learning strategies for designing potent antimicrobial peptides

BACKGROUND

Current methods in machine learning provide approaches for solving challenging, multiple constraint design problems. While deep learning and related neural networking methods have state-of-the-art performance, their vulnerability in decision making processes leading to irrational outcomes is a major concern for their implementation. With the rising antibiotic resistance, antimicrobial peptides (AMPs) have increasingly gained attention as novel therapeutic agents. This challenging design problem requires peptides which meet the multiple constraints of limiting drug-resistance in bacteria, preventing secondary infections from imbalanced microbial flora, and avoiding immune system suppression. AMPs offer a promising, bioinspired design space to targeting antimicrobial activity, but their versatility also requires the curated selection from a combinatorial sequence space. This space is too large for brute-force methods or currently known rational design approaches outside of machine learning. While there has been progress in using the design space to more effectively target AMP activity, a widely applicable approach has been elusive. The lack of transparency in machine learning has limited the advancement of scientific knowledge of how AMPs are related among each other, and the lack of general applicability for fully rational approaches has limited a broader understanding of the design space.

METHODS

Here we combined an evolutionary method with rough set theory, a transparent machine learning approach, for designing antimicrobial peptides (AMPs). Our method achieves the customization of AMPs using supervised learning boundaries. Our system employs in vitro bacterial assays to measure fitness, codon-representation of peptides to gain flexibility of sequence selection in DNA-space with a genetic algorithm and machine learning to further accelerate the process.

RESULTS

We use supervised machine learning and a genetic algorithm to find a peptide active against S. epidermidis, a common bacterial strain for implant infections, with an improved aggregation propensity average for an improved ease of synthesis.

CONCLUSIONS

Our results demonstrate that AMP design can be customized to maintain activity and simplify production. To our knowledge, this is the first time when codon-based genetic algorithms combined with rough set theory methods is used for computational search on peptide sequences.

Review on the occurrence of the mcr-1 gene causing colistin resistance in cow's milk and dairy products

Both livestock farmers and the clinic use significant amount of antibiotics worldwide, in many cases the same kind. Antibiotic resistance is not a new phenomenon, however, it is a matter of concern that resistance genes (mcr - Mobilized Colistin Resistance - genes) that render last-resort drugs (Colistin) ineffective, have already evolved. Nowadays, there is a significant consumption of milk and dairy products, which, if not treated properly, can contain bacteria (mainly Gram-negative bacteria). We collected articles and reviews in which Gram-negative bacteria carrying the mcr-1 gene have been detected in milk, dairy products, or cattle. Reports have shown that although the incidence is still low, unfortunately the gene has been detected in some dairy products on almost every continent. In the interest of our health, the use of colistin in livestock farming must be banned as soon as possible, and new treatments should be applied so that we can continue to have a chance in fighting multidrug-resistant bacteria in human medicine.

Targeting the ATP Synthase in Staphylococcus aureus Small Colony Variants, Streptococcus pyogenes and Pathogenic Fungi

The ATP synthase has been validated as a druggable target with the approval of the ATP synthase inhibitor, bedaquiline, for treatment of drug-resistant Mycobacterium tuberculosis, a bacterial species in which the ATP synthase is essential for viability. Gene inactivation studies have also shown that the ATP synthase is essential among Streptococci, and some studies even suggest that inhibition of the ATP synthase is a strategy for the elimination of Staphylococcus aureus small colony variants with deficiencies in the electron transport chain, as well as pathogenic fungi, such as Candida albicans. Here we investigated five structurally diverse ATP synthase inhibitors, namely N,N′-dicyclohexylcarbodiimide (DCCD), oligomycin A, tomatidine, resveratrol and piceatannol, for their growth inhibitory activity against the bacterial strains Streptococcus pyogenes, S. aureus and two isogenic small colony variants, as well as the pathogenic fungal species, C. albicans and Aspergillus niger. DCCD showed broad-spectrum inhibitory activity against all the strains (minimum inhibitory concentration (MIC) 2–16 µg/mL), except for S. aureus, where the ATP synthase is dispensable for growth. Contrarily, oligomycin A selectively inhibited the fungal strains (MIC 1–8 µg/mL), while tomatidine showed very potent, but selective, activity against small colony variants of S. aureus with compromised electron transport chain activity (MIC 0.0625 µg/mL). Small colony variants of S. aureus were also more sensitive to resveratrol and piceatannol than the wild-type strain, and piceatannol inhibited S. pyogenes at 16–32 µg/mL. We previously showed that transposon inactivation of the ATP synthase sensitizes S. aureus towards polymyxin B and colistin, and here we demonstrate that treatment with structurally diverse ATP synthase inhibitors sensitized S. aureus towards polymyxin B. Collectively, our data show that ATP synthase inhibitors can have selective inhibitory activity against pathogenic microorganisms in which the ATP synthase is essential. The data also show that the inhibition of the ATP synthase in Streptococcus pyogenes may be a new strategy for development of a narrow-spectrum antibiotic class. In other major bacterial pathogens, such as S. aureus and potentially Escherichia coli, where the ATP synthase is dispensable, the ATP synthase inhibitors may be applied in combination with antimicrobial peptides to provide new therapeutic options.

Plasmid Dynamics of mcr-1-Positive Salmonella spp. in a General Hospital in China

Salmonella is an important food pathogen that can cause severe gastroenteritis with more than 600,000 deaths globally every year. Colistin (COL), a last-resort antibiotic, is ineffective in bacteria that carry a functional mcr-1 gene, which is often spread by conjugative plasmids. Our work aimed to understand the prevalence of the mcr-1 gene in clinical isolates of Salmonella, as the frequency of occurrence of the mcr-1 gene is increasing globally. Therefore, we analyzed 689 clinical strains, that were isolated between 2009 and late 2018. The mcr-1 gene was found in six strains, which we analyzed in detail by whole genome sequencing and antibiotic susceptibility testing, while we also provide the clinical information on the patients suffering from an infection. The genomic analysis revealed that five strains had plasmid-encoded mcr-1 gene located in four IncHI2 plasmids and one IncI2 plasmid, while one strain had the chromosomal mcr-1 gene originated from plasmid. Surprisingly, in two strains the mcr-1 genes were inactive due to disruption by insertion sequences (ISs): ISApl1 and ISVsa5. A detailed analysis of the plasmids revealed a multitude of ISs, most commonly IS26. The IS contained genes that meditate broad resistance toward most antibiotics underlining their importance of the mobile elements, also with respect to the spread of the mcr-1 gene. Our study revealed potential reservoirs for the transmission of COL resistance and offers insights into the evolution of the mcr-1 gene in Salmonella.

Detection of Five mcr-9-Carrying Enterobacterales Isolates in Four Czech Hospitals

The aim of this study was to report the characterization of the first mcr-positive Enterobacterales isolated from Czech hospitals. In 2019, one Citrobacter freundii and four Enterobacter isolates were recovered from Czech hospitals. The production of carbapenemases was examined by a matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) imipenem hydrolysis assay. Additionally, bacteria were screened for the presence of carbapenemase-encoding genes and plasmid-mediated colistin resistance genes by PCR. To define the genetic units carrying mcr genes, the genomic DNAs of mcr-carrying clinical isolates were sequenced on the PacBio Sequel I platform. Results showed that all isolates carried blaVIM- and mcr-like genes. Analysis of whole-genome sequencing (WGS) data revealed that all isolates carried mcr-9-like alleles. Furthermore, the three sequence type 106 (ST106) Enterobacter hormaechei isolates harbored the blaVIM-1 gene, while the ST764 E. hormaechei and ST95 C. freundii included blaVIM-4 Analysis of plasmid sequences showed that, in all isolates, mcr-9 was carried on IncHI2 plasmids. Additionally, at least one multidrug resistance (MDR) region was identified in each mcr-9-carrying IncHI2 plasmid. The blaVIM-4 gene was found in the MDR regions of p48880_MCR_VIM and p51929_MCR_VIM. In the three remaining isolates, blaVIM-1 was localized on plasmids (∼55 kb) exhibiting repA-like sequences 99% identical to the respective gene of pKPC-CAV1193. In conclusion, to the best of our knowledge, these 5 isolates were the first mcr-9-positive bacteria of clinical origin identified in the Czech Republic. Additionally, the carriage of the blaVIM-1 on pKPC-CAV1193-like plasmids is described for the first time. Thus, our findings underline the ongoing evolution of mobile elements implicated in the dissemination of clinically important resistance determinants.IMPORTANCE Infections caused by carbapenemase-producing bacteria have led to the revival of polymyxins as the "last-resort" antibiotic. Since 2016, several reports describing the presence of plasmid-mediated colistin resistance genes, mcr, in different host species and geographic areas were published. Here, we report the first detection of Enterobacterales carrying mcr-9-like alleles isolated from Czech hospitals in 2019. Furthermore, the three ST106 Enterobacter hormaechei isolates harbored blaVIM-1, while the ST764 E. hormaechei and ST95 Citrobacter freundii isolates included blaVIM-4 Analysis of WGS data showed that, in all isolates, mcr-9 was carried on IncHI2 plasmids. blaVIM-4 was found in the MDR regions of IncHI2 plasmids, while blaVIM-1 was localized on pKPC-CAV1193-like plasmids, described here for the first time. These findings underline the ongoing evolution of mobile elements implicated in dissemination of clinically important resistance determinants. Thus, WGS characterization of MDR bacteria is crucial to unravel the mechanisms involved in dissemination of resistance mechanisms.

Emergence of plasmid-mediated mcr genes from Gram-negative bacteria at the human-animal interface

BACKGROUND

The global emergence of plasmid-mediated colistin resistance (Col-R) conferred by mcr genes in gram-negative rods (GNRs) has jeopardized the last treatment option for multidrug-resistant bacterial infections in humans. This study aimed to assess the emergence of mcr gene-mediated Col-R in GNRs isolated from humans and animals in Pakistan.

METHODS

Animal and clinical specimens collected from various sources were prospectively analysed using standard microbiological procedures. Pathogens were identified using the API 20E and API 20NE systems (bioMerieux). Minimum inhibitory concentration (MIC) against colistin was determined using the MIC detection methods, and multiplex polymerase chain reaction (PCR) was used to amplify the mcr-1 to mcr-5 genes.

RESULTS

We isolated 126 (88.1%) animal and 17 (11.9%) human Col-R phenotypes, among which there was a significant association (P < 0.01) of Escherichia coli and Proteus mirabilis with animals and of Acinetobacter baumannii with humans. Animal strains exhibited statistically significant (P < 0.05) resistance to co-trimoxazole, chloramphenicol, and moxifloxacin, and the human pathogens exhibited statistically significant (P < 0.05) antibiotic resistance to cephalosporins, carbapenems, and piperacillin-tazobactam. For Col-R strains, MIC₅₀ values were > 6 µg/mL and > 12 µg/mL for human and animal isolates, respectively. mcr genes were detected in 110 (76.9%) bacterial strains, of which 108 (98.2%) were mcr-1 and 2 (1.8%) were mcr-2.

CONCLUSIONS

The detection of a considerable number of mcr-1 and mcr-2 genes in animals is worrisome, as they are now being detected in clinical pathogens. The acquisition of mcr genes by colistin-susceptible bacteria could leave us in a post-antibiotic era.

Association of the colistin resistance gene mcr-1 with faecal pollution in water environments in Hanoi, Vietnam

Colistin is one of the antibiotics of last resort for human health. However, the dissemination of the plasmid-mediated colistin resistance gene mcr-1 is of great concern globally. In the One Health framework, the environment is an important component for managing antimicrobial resistance. However, little information is available concerning the prevalence of mcr-1 in water environments. We aimed to reveal the prevalence of mcr-1 in different water environments in Hanoi, Vietnam. Quantitative PCR was applied to detect mcr-1 in four urban drainages receiving untreated domestic wastewater, three rivers, five lakes and two groundwater samples. Urban drainages contained higher concentrations of mcr-1, suggesting that urban residents carry the gene. The class 1 integron-integrase gene was identified as a good surrogate of antibiotic resistance genes including mcr-1. A significant correlation was found between the levels of mcr-1 and the human-specific cross-assembly phage, which is an indicator of human faecal pollution. These results indicated that the primary source of mcr-1 in urban water environments is human faeces, which is consistent with the fact that most domestic wastewater is untreated in Hanoi. The control of untreated wastewater is critical for alleviating the spread of mcr-1 in water environments in Vietnam.

Antibiogram Profiles and Risk Factors for Multidrug Resistance of Salmonella enterica Recovered from Village Chickens (Gallus gallus domesticus Linnaeus) and Other Environmental Sources in the Central and Southern Peninsular Malaysia

The emergence of multidrug resistance (MDR), including colistin resistance, among Enterobacteriaceae recovered from food animals poses a serious public health threat because of the potential transmission of these resistant variants to humans along the food chain. Village chickens or Ayam Kampung are free-range birds and are preferred by a growing number of consumers who consider these chickens to be organic and more wholesome. The current study investigates the antibiogram profiles of Salmonella isolates recovered from village chicken flocks in South-central Peninsular Malaysia. A total of 34 isolates belonging to eight serotypes isolated from village chickens were screened for resistance towards antimicrobials including colistin according to the WHO and OIE recommendations of critical antibiotics. S. Weltevreden accounted for 20.6% of total isolates, followed by serovars Typhimurium and Agona (17.6%). The majority of isolates (73.5%) demonstrated resistance to one or more antimicrobials. Eight isolates (23.5%) were resistant to ≥3 antimicrobial classes. Colistin resistance (minimum inhibitory concentrations: 4-16 mg/L) was detected among five isolates (14.7%), including S. Weltevreden, S. Albany, S. Typhimurium, and Salmonella spp. Univariable analysis of risk factors likely to influence the occurrence of MDR Salmonella revealed that the flock size, poultry production system, and use of antibiotics in the farm were not significantly (p > 0.05) associated with MDR Salmonella. The current study highlights that MDR Salmonella occur at a lower level in village chickens compared to that found in live commercial chickens. However, MDR remains a problem even among free-range chickens with minimal exposure to antibiotics.

Plasmidic resistance to colistin mediated by mcr-1 gene in Escherichia coli clinical isolates in Argentina: A retrospective study, 2012-2018

Objective.

To describe the resistance profile and the genetic characteristics of Escherichia coli isolates that harbor the mobilizable colistin resistance gene mcr-1 in Argentina.

Methods.

This was a retrospective study of 192 E. coli isolates positive for mcr-1 obtained from 69 hospitals of Buenos Aires City and 14 Argentinean provinces in 2012 – 2018. The antimicrobial susceptibility was performed by agar diffusion, broth macrodilution, and/or agar dilution. Standard polymerase chain reaction (PCR) was performed to detect resistance genes and incompatibility groups; specific PCR was applied to discriminate between blaCTX-M allelic groups and mcr-1.5 variant. The genetic relatedness among isolates was evaluated by XbaI-pulsed field gel electrophoresis and multilocus sequence typing in a subset of isolates.

Results.

All E. coli isolates showed minimal inhibitory concentrations to colistin ≥ 4μg/mL; nearly 50% were resistant to third-generation cephalosporins, with CTX-M-2 being the main extended-spectrum β-lactamase detected. Five E. coli were carbapenemase-producers (3 NDM, 2 KPC). The mcr-1.5 variant was detected in 13.5% of the isolates. No genetic relationship was observed among the mcr-1-positive E. coli clinical isolates, but a high proportion (164/192; 85.4%) of IncI2 plasmids was detected.

Conclusions.

The presence of IncI2 plasmids among highly diverse E. coli clones suggests that the mcr-1 gene’s wide distribution in Argentina may be driven by the horizontal transmission of IncI2 plasmids.

Eight years of sales surveillance of antimicrobials for veterinary use in Germany-What are the perceptions?

A surveillance system for sales volumes of antimicrobial agents for veterinary use was established in Germany in 2011. Since then, pharmaceutical companies and wholesalers have been legally obliged to report annual volumes of veterinary antimicrobial products sold to veterinary practices or clinics located in Germany. The evaluation of sales volumes for eight consecutive years resulted in a considerable total decrease by 58% from 1706 tons to 722 tons. During the investigation period, two legally binding measures to control the risk of antimicrobial resistance resulting from the veterinary use of antimicrobials were introduced, a) the German treatment frequencies benchmarking in 2014 and b) the obligation to conduct susceptibility testing for the use of cephalosporins of the 3^rd and 4^th generation and of fluoroquinolones in 2018. Both had a marked impact on sales volumes. Nonetheless, the category of Critically Important Antimicrobials as defined by the World Health Organization kept accounting for the highest share on sales volumes in Germany in 2018 with 403 tons, despite an overall reduction by 53%. Sales surveillance is considered essential for data retrieval on a global scale and inter-country comparison. However, the usability of a surveillance system based on sales data for risk management of antimicrobial resistance has limitations. The German system does not include off-label use of antimicrobial products authorized for human medicine and does not allow for identification of areas of high risk according to animal species, farm and production types and indications for treatment. For further reduction and enhanced promotion of a prudent use of antimicrobials, targeted measures would be required that could only be deducted from use data collected at farm or veterinary practice level. A surveillance system based on use data is currently lacking in Germany but will be established according to Regulation (EU) 2019/6 on veterinary medicinal products.

Multidrug Resistance (MDR) and Collateral Sensitivity in Bacteria, with Special Attention to Genetic and Evolutionary Aspects and to the Perspectives of Antimicrobial Peptides-A Review

Antibiotic poly-resistance (multidrug-, extreme-, and pan-drug resistance) is controlled by adaptive evolution. Darwinian and Lamarckian interpretations of resistance evolution are discussed. Arguments for, and against, pessimistic forecasts on a fatal “post-antibiotic era” are evaluated. In commensal niches, the appearance of a new antibiotic resistance often reduces fitness, but compensatory mutations may counteract this tendency. The appearance of new antibiotic resistance is frequently accompanied by a collateral sensitivity to other resistances. Organisms with an expanding open pan-genome, such as Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae, can withstand an increased number of resistances by exploiting their evolutionary plasticity and disseminating clonally or poly-clonally. Multidrug-resistant pathogen clones can become predominant under antibiotic stress conditions but, under the influence of negative frequency-dependent selection, are prevented from rising to dominance in a population in a commensal niche. Antimicrobial peptides have a great potential to combat multidrug resistance, since antibiotic-resistant bacteria have shown a high frequency of collateral sensitivity to antimicrobial peptides. In addition, the mobility patterns of antibiotic resistance, and antimicrobial peptide resistance, genes are completely different. The integron trade in commensal niches is fortunately limited by the species-specificity of resistance genes. Hence, we theorize that the suggested post-antibiotic era has not yet come, and indeed might never come.

Circumventing antimicrobial-resistance and preventing its development in novel, bacterial infection-control strategies

INTRODUCTION

Development of new antimicrobials with ever 'better' bacterial killing has long been considered the appropriate response to the growing threat of antimicrobial-resistant infections. However, the time-period between the introduction of a new antibiotic and the appearance of resistance amongst bacterial pathogens is getting shorter and shorter. This suggests that alternative pathways than making ever 'better' antimicrobials should be taken.

AREAS COVERED

This review aims to answer the questions (1) whether we have means to circumvent existing antibiotic-resistance mechanisms, (2) whether we can revert existing antibiotic-resistance, (3) how we can prevent the development of antimicrobial-resistance against novel infection-control strategies, including nano-antimicrobials.

EXPERT OPINION

Relying on relieving antibiotic-pressure and natural outcompeting of antimicrobial-resistant bacteria seems an uncertain way out of the antibiotic-crisis facing us. Novel, non-antibiotic, nanotechnology-based infection control-strategies are promising. At the same time, rapid development of new resistance mechanisms once novel strategies is taken into global clinical use, may not be ruled out and must be closely monitored. This suggests focusing research and development on designing suitable combinations of existing antibiotics with new nano-antimicrobials in a way that induction of new antimicrobial-resistance mechanisms is avoided. The latter suggestion, however, requires a change of focus in research and development.

Emergence of mcr-9.1 in Extended-Spectrum-β-Lactamase-Producing Clinical Enterobacteriaceae in Pretoria, South Africa: Global Evolutionary Phylogenomics, Resistome, and Mobilome

Extended-spectrum-β-lactamase (ESBL)-producing Enterobacteriaceae are critical-priority pathogens that cause substantial fatalities. With the emergence of mobile mcr genes mediating resistance to colistin in Enterobacteriaceae, clinicians are now left with few therapeutic options. Eleven clinical Enterobacteriaceae strains with resistance to cephems and/or colistin were genomically analyzed to determine their resistomes, mobilomes, and evolutionary relationships to global strains. The global phylogenomics of mcr genes and mcr-9.1-bearing genomes were further analyzed. Ten isolates were ESBL positive. The isolates were multidrug resistant and phylogenetically related to global clones but distant from local strains. Multiple resistance genes, including bla _CTX-M-15 bla _TEM-1, and mcr-9.1, were found in single isolates; ISEc9, IS19, and Tn3 transposons bracketed bla _CTX-M-15 and bla _TEM-1 Common plasmid types included IncF, IncH, and ColRNAI. mcr-9 was of close sequence identity to mcr-3, mcr-5, mcr-7, mcr-8, and mcr-10. Genomes bearing mcr-9.1 clustered into six main phyletic groups (A to F), with those of this study belonging to clade B. Enterobacter species and Salmonella species are the main hosts of mcr-9.1 globally, although diverse promiscuous plasmids disseminate mcr-9.1 across different bacterial species. Emergence of mcr-9.1 in ESBL-producing Enterobacteriaceae in South Africa is worrying, due to the restricted therapeutic options. Intensive One Health molecular surveillance might discover other mcr alleles and inform infection management and antibiotic choices.IMPORTANCE Colistin is currently the last-resort antibiotic for difficult-to-treat bacterial infections. However, colistin resistance genes that can move from bacteria to bacteria have emerged, threatening the safe treatment of many bacterial infections. One of these genes, mcr-9.1, has emerged in South Africa in bacteria that are multidrug resistant, further limiting treatment options for clinicians. In this work, we show that this new gene is disseminating worldwide through Enterobacter and Salmonella species through multiple plasmids. This worrying observation requires urgent action to prevent further escalation of this gene in South Africa and Africa.

Preventive antibiotic treatment of calves: emergence of dysbiosis causing propagation of obese state-associated and mobile multidrug resistance-carrying bacteria

In agriculture, antibiotics are used for the treatment and prevention of livestock disease. Antibiotics perturb the bacterial gut composition but the extent of these changes and potential consequences for animal and human health is still debated. Six calves were housed in a controlled environment. Three animals received an injection of the antibiotic florfenicol (Nuflor), and three received no treatment. Faecal samples were collected at 0, 3 and 7 days, and bacterial communities were profiled to assess the impact of a therapy on the gut microbiota. Phylogenetic analysis (16S-rDNA) established that at day 7, antibiotic-treated microbiota showed a 10-fold increase in facultative anaerobic Escherichia spp, a signature of imbalanced microbiota, dysbiosis. The antibiotic resistome showed a high background of antibiotic resistance genes, which did not significantly change in response to florfenicol. However, the maintenance of Escherichia coli plasmid-encoded quinolone, oqxB and propagation of mcr-2, and colistin resistance genes were observed and confirmed by Sanger sequencing. The microbiota of treated animals was enriched with energy harvesting bacteria, common to obese microbial communities. We propose that antibiotic treatment of healthy animals leads to unbalanced, disease- and obese-related microbiota that promotes growth of E. coli carrying resistance genes on mobile elements, potentially increasing the risk of transmission of antibiotic resistant bacteria to humans.

Winter is coming - Impact of temperature on the variation of beta-lactamase and mcr genes in a wastewater treatment plant

Wastewater treatment plants (WWTP) play a key role in the dissemination of antibiotic resistance and analyzing the abundance of antibiotic resistance genes (ARGs) and resistant bacteria is necessary to evaluate the risk of proliferation caused by WWTPs. Since few studies investigated the seasonal variation of antibiotic resistance, this study aimed to determine the abundance of beta-lactamase and mcr genes and to characterize phenotypic resistant strains in a WWTP in Germany over the seasons. Wastewater, sewage sludge and effluent samples were collected over a one year period and analyzed using quantitative real-time PCR. Resistant strains were isolated, followed by identification and antibiotic susceptibility testing using VITEK 2. The results show a significantly higher occurrence of nearly all investigated ARGs in the wastewater compared to sewage sludge and effluent. ARG abundance and temperature showed a negative correlation in wastewater and significant differences between ARG abundance during warmer and colder seasons were determined, indicating a seasonal effect. Co-occurrence of mcr-1 and carbapenemase genes in a multi-drug resistant Enterobacter cloacae and Escherichia coli producing extended-spectrum beta-lactamase (ESBL) was determined. To the best of our knowledge, this is the first detection of mcr-1, bla_VIM and bla_OXA-48 in an ESBL-producing E. coli. Although wastewater treatment reduced the abundance of ARGs and resistant strains, a dissemination into the river might be possible because carbapenemase-, CTX-M- and mcr-1-gene harboring strains were still present in the effluent.

Molecular epidemiology and mechanisms of antibiotic resistance in Enterococcus spp., Staphylococcus spp., and Streptococcus spp. in Africa: a systematic review from a One Health perspective

A systematic review of antibiotic-resistant Gram-positive bacteria in Africa from a One Health perspective is lacking. Here, we report result from a search for English-language articles on the resistance mechanisms and clonality of Gram-positive bacteria in Africa between 2007 and 2019 reported in PubMed, Web of Science, ScienceDirect, and African Journals OnLine; 172 studies from 22 different African countries were identified. Resistance genes, such as mecA, erm(B), erm(C), tet(M), tet(K), tet(L), vanB, vanA, vanC, and tet(O), were found to be common. Staphylococcus spp., Enterococcus spp., and Streptococcus spp. were the main species reported by the studies, with clones such as Staphylococcus aureus ST5 (n = 218 isolates), ST8 (n = 127 isolates), ST80 (n = 133 isolates), and ST88 (n = 117 isolates), and mobile genetic elements such as IS16 (n = 28 isolates), IS256 (n = 96), Tn916 (n = 107 isolates), and SCCmec (n = 4437 isolates) identified. SCCmec IV (n = 747 isolates) was predominant, followed by SCCmec III (n = 305 isolates), SCCmec II (n = 163 isolates), SCCmec V (n = 135 isolates), and SCCmec I (n = 79 isolates). Resistance to penicillin (n = 5926 isolates), tetracycline (n = 5300 isolates), erythromycin (n = 5151 isolates), rifampicin (n = 3823 isolates), gentamycin (n = 3494 isolates), sulfamethoxazole/trimethoprim (n = 3089 isolates), and ciprofloxacin (n = 2746 isolates) was common in most reports from 22 countries. Clonal dissemination of resistance across countries and between humans, animals, and the environment was observed. Resistance rates ranged from 1.4% to 100% for 15 of the studies; 10 were One Health-related studies. Strict infection control measures, antimicrobial stewardship, and periodic One Health epidemiological surveillance studies are needed to monitor and contain the threat of increasing antibiotic resistance in Africa.

An in silico analysis of acquired antimicrobial resistance genes in Aeromonas plasmids

Sequences of 105 Aeromonas species plasmids were probed for acquired anti-microbial resistance (AMR) genes using a bioinformatics approach. The plasmids showed no positive linear correlation between size and GC content and up to 55 acquired AMR genes were found in 39 (37%) plasmids after in silico screening for resistance against 15 antibiotic drug classes. Overall, potential multiple antibiotic resistance (p-MAR) index ranged from 0.07 to 0.53. Up to 18 plasmids were predicted to mediate multiple drug resistance (MDR). Plasmids pS121-1a (A. salmonicida), pWCX23_1 (A. hydrophila) and pASP-a58 (A. veronii) harboured 18, 15 and 14 AMR genes respectively. The five most occurring drug classes for which AMR genes were detected were aminoglycosides (27%), followed by beta-lactams (17%), sulphonamides (13%), fluoroquinolones (13%), and phenicols (10%). The most prevalent genes were a sulphonamide resistant gene Sul1, the gene aac (6')-Ib-cr (aminoglycoside 6'-N-acetyl transferase type Ib-cr) resistant to aminoglycosides and the blaKPC-2 gene, which encodes carbapenemase-production. Plasmid acquisition of AMR genes was mainly inter-genus rather than intra-genus. Eighteen plasmids showed template or host genes acquired from Pseudomonas monteilii, Salmonella enterica or Escherichia coli. The most occurring antimicrobial resistance determinants (ARDs) were beta-lactamase, followed by aminoglycosides acetyl-transferases, and then efflux pumps. Screening of new isolates in vitro and in vivo is required to ascertain the level of phenotypic expression of colistin and other acquired AMR genes detected.

Retrospective Screening and Analysis of mcr-1 and bla NDM in Gram-Negative Bacteria in China, 2010-2019

Currently, Gram-negative bacteria have developed multidrug and broad-spectrum drug resistance, and the numbers of species and strains carrying mcr or bla_NDM genes are increasing. In this study, mcr-1 and bla_NDM distribution of 12,858 Gram-negative bacteria isolated from wildlife, patients, livestock, poultry and environment in 14 provinces of China from 2010 to 2019 and the antibiotics resistance in regard to polymyxins (polymyxin B and colistin) and carbapenems of positive strains were investigated. A total of 70 strains of 10 species carried the mcr-1 gene, positive rates of patients, livestock and poultry, and environmental strains were 0.62% (36/5,828), 4.07% (29/712), 5.43% (5/92), respectively. Six strains of 3 species carrying the bla_NDM gene all came from patients 0.10% (6/5,828). Two new mcr-1 gene variants (GenBank: MK965883, MK965884) were identified, one of which contains premature stop codon. The drug susceptibility results showed that all mcr-1 carriers were sensitive to carbapenems, among which, 66 strains were resistant and 4 were sensitive to polymyxins. The strains with the bla_NDM gene had different degrees of resistance to carbapenems and were sensitive to polymyxins. The findings that species carrying mcr-1 or bla_NDM genes were limited and mostly normal flora of opportunistic or low pathogenic organisms indicated that transfer of mcr-1 and bla_NDM genes between bacteria was relatively limited in China. The none detection among wildlife compared with other sources supports the speculation that the emergence of and increase in polymyxins and carbapenem-resistant strains was mainly related to the selective pressure of antibiotics.

Occurrence and Characteristics of Mobile Colistin Resistance (mcr) Gene-Containing Isolates from the Environment: A Review

The emergence and spread of mobile colistin (COL) resistance (mcr) genes jeopardize the efficacy of COL, a last resort antibiotic for treating deadly infections. COL has been used in livestock for decades globally. Bacteria have mobilized mcr genes (mcr-1 to mcr-9). Mcr-gene-containing bacteria (MGCB) have disseminated by horizontal/lateral transfer into diverse ecosystems, including aquatic, soil, botanical, wildlife, animal environment, and public places. The mcr-1, mcr-2, mcr-3, mcr-5, mcr-7, and mcr-8 have been detected in isolates from and/or directly in environmental samples. These genes are harboured by Escherichia coli, Enterobacter, Klebsiella, Proteus, Salmonella, Citrobacter, Pseudomonas, Acinetobacter, Kluyvera, Aeromonas, Providencia, and Raulotella isolates. Different conjugative and non-conjugative plasmids form the backbones for mcr in these isolates, but mcr have also been integrated into the chromosome of some strains. Insertion sequences (IS) (especially ISApl1) located upstream or downstream of mcr, class 1–3 integrons, and transposons are other drivers of mcr in the environment. Genes encoding multi-/extensive-drug resistance and virulence are often co-located with mcr on plasmids in environmental isolates. Transmission of mcr to/among environmental strains is clonally unrestricted. Contact with the mcr-containing reservoirs, consumption of contaminated animal-/plant-based foods or water, international animal-/plant-based food trades and travel, are routes for transmission of MGCB.

Intestinal carriage of colistin resistant Enterobacteriaceae in hospitalized patients from an Indian center

There is limited data on the gut colonization rate of colistin resistant (Col-R) bacteria in patients and healthy volunteers in India. Aim of this study was to investigate the stool carriage rate of Col-R in hospitalized patients. Stool samples were inoculated in Eosin Methylene Blue agar plates supplemented with colistin. Colistin minimum inhibitory concentrations (MICs) were determined by the broth microdilution method. PCR for the mcr-1 was performed on Col-R Enterobacteriaceae isolates. Mutations in the mgrB gene were analyzed in K. pneumoniae isolates. Mcr-1 positive E. coli was subjected to whole-genome sequencing. Out of 65 stool samples screened, 33 (51%) samples carried Col-R bacteria. Majority (76.7%) of the isolates were sensitive to carbapenem.

Molecular epidemiology of mcr gene group

Colistin and polymyxin B are the “last reserve” antimicrobials for the treatment of extensively drug-resistant Gram-negative bacterial infections. The rapidly increasing prevalence of polymyxin resistance mediated by the mcr gene localized on plasmid DNA currently poses a high epidemiological threat. In order to control a distribution of mcr genes, it is necessary to develop highly accurate, highly sensitive and easy-to-use diagnostic tools. This paper provides a review of the most relevant studies on the molecular epidemiology as well as current approaches to microbiological and molecular detection of mcr group genes.

Global geographic trends in antimicrobial resistance: the role of international travel

BACKGROUND

Rising antimicrobial resistance (AMR) is a threat to modern medicine, and increasing international mobility facilitates the spread of AMR. Infections with resistant organisms have higher morbidity and mortality, are costlier to treat, result in longer hospital stays and place a greater burden on health systems than infections caused by susceptible organisms. Here we review the role of travel in the international dissemination of AMR and consider actions at the levels of travelers, travel medicine practitioners and policymakers that would mitigate this threat.

RESULTS

Resistant pathogens do not recognize international borders; travelers to areas with high AMR prevalence are likely to be exposed to resistant bacteria and return to their home countries colonized. Medical tourists go between health facilities with drastically different rates of AMR, potentially transmitting highly resistant strains.Drug-resistant bacteria have been found in every continent; however, differences between countries in the prevalence of AMR depend on multiple factors. These include levels of antibiotic consumption (including inappropriate use), access to clean water, adequate sanitation, vaccination coverage, the availability of quality healthcare and access to high-quality medical products.

CONCLUSIONS

Travelers to areas with high levels of AMR should have vaccines up to date, be aware of ways of treating and preventing travelers' diarrhea (other than antibiotic use) and be informed on safe sexual practices. The healthcare systems of low- and middle-income countries require investment to reduce the transmission of resistant strains by improving access to clean water, sanitation facilities and vaccines. Efforts are needed to curb inappropriate antibiotic use worldwide. In addition, more surveillance is needed to understand the role of the movement of humans, livestock and food products in resistance transmission. The travel medicine community has a key role to play in advocating for the recognition of AMR as a priority on the international health agenda.

KEY POLICY RECOMMENDATIONS

AMR is a threat to modern medicine, and international travel plays a key role in the spread of highly resistant strains. It is essential that this is addressed at multiple levels. Individual travelers can reduce antibiotic consumption and the likelihood of infection. Travelers should have up-to-date vaccines and be informed on methods of preventing and treating travelers' diarrhea, other than use of antibiotics and on safe sexual practices, such as condom use. Healthcare facilities need to be aware of the travel history of patients to provide appropriate treatment to those who are at high risk of exposure and to prevent further spread. Internationally, in countries without reliable and universal access to clean water, sanitation and hygiene, investment is needed to reduce the emergence and spread of resistance and ensure the antimicrobials available are of assured quality. High-income countries must ensure their use of antimicrobials is appropriate to reduce selection for AMR. Surveillance across all countries is needed to monitor and respond to this emerging threat.

Dissemination and Comparison of Genetic Determinants of mcr-Mediated Colistin Resistance in Enterobacteriaceae via Retailed Raw Meat Products

The global food chain may significantly promote the dissemination of bacteria resistant to antibiotics around the world. This study was aimed at determining the prevalence and genetic characteristics of Enterobacteriaceae with mcr-mediated colistin (CT) resistance in retail meat of different origins. Bacteria of the Enterobacteriaceae family carrying the mcr-1 gene were detected in 21% (18/86) of the examined samples, especially in turkey meat and liver originating from EU and non-EU countries (19%) and in rabbit meat imported from China (2%). The examined samples of the meat and liver of chicken and other poultry and of pork and beef were negative for the presence of bacteria carrying the mcr-1 to mcr-5 genes. A huge number of isolates belonging to Escherchia coli (n = 54), Klebsiella pneumoniae (n = 6), and Citrobacter braakii (n = 1) carrying the mcr-1 gene were obtained. Despite the high heterogeneity of the tested isolates, the mcr-1 gene was localized on only three types of plasmids (IncX4, IncHI2, and IncI2). The most frequent type of plasmid was IncX4, which carried the mcr-1 gene in 77% of E. coli and K. pneumoniae isolates from turkey meat and liver samples from the Czechia, Germany, Poland, and Brazil. Our findings indicate highly probable interspecies transfer of IncX4 and IncI2 plasmids within one meat sample. The co-resistance of plasmid-mediated CT resistance encoded by the mcr-1 and ESBL genes was detected in 18% of the isolates. Another noteworthy finding was the fosA3 gene coding for fosfomycin resistance in a multidrug-resistant isolate of E. coli from rabbit meat imported from China. The observed high level of Enterobacteriaceae with plasmids carrying the mcr-1 gene in retail meat reflects the need for Europe-wide monitoring of mcr-mediated CT resistance throughout the whole food chain.

An overview of colistin resistance, mobilized colistin resistance genes dissemination, global responses, and the alternatives to colistin: A review

Colistin, also known as polymyxin E, is an antimicrobial agent that is effective against a variety of Gram-negative bacilli, especially the Enterobacteriaceae family. Recently, the wide dissemination of colistin-resistance has brought strong attention to the scientific society because of its importance as the last resort for the treatment of carbapenem-resistant Enterobacteriaceae infections and its possible horizontal transmission. The mobilized colistin resistance (mcr) gene was identified as the gene responsible for unique colistin resistance. Indeed, despite many studies that have revealed a pan variation in the existence of this gene, not only for the mcr genes main group but also for its many subgroups, the problem is growing and worsening day after day. In this regard, this review paper is set to review the updated data that has been published up to the end of 2019 third quarter, especially when related to colistin resistance by the mcr genes. It will include the present status of colistin resistance worldwide, the mcr gene dissemination in different sectors, the discovery of the mcr variants, and the global plan to deal with the threat of antimicrobial resistance. In line with global awareness, and to stop antibiotic misuse and overuse, especially in agricultural animals, the study will further discuss in detail the latest alternatives to colistin use in animals, which may contribute to the elimination of inappropriate antibiotic use and to the help in preventing infections. This review will advance our understanding of colistin resistance, while supporting the efforts toward better stewardship, for the proper usage of antimicrobial drugs in humans, animals, and in the environment.

Comparative evaluation of microscan walkaway 96 plus ID/AST system and mikrolatest broth microdilution kit in assessing In vitro colistin susceptibility of carbapenem-resistant clinical gram-negative bacterial isolates: Experience from a tertiary care teaching hospital in Rishikesh, Uttarakhand

Context

As reports on colistin resistance are slowly emerging from different parts of the world, it is imperative that the clinical microbiology laboratories should generate accurate in vitro colistin susceptibility results.

Aim

The aim is to generate preliminary data on the diagnostic utility of MicroScan WalkAway 96 Plus Identification ID/ Antimicrobial susceptibility testing AST system in determining in vitro colistin susceptibility of carbapenem-resistant clinical Gram-negative bacterial isolates.

Settings and Design

A pilot study was conducted in a tertiary care teaching hospital located in Rishikesh, Uttarakhand, between May and June 2019.

Materials and Methods

Thirty-four carbapenem-resistant Escherichia coli, Pseudomonas aeruginosa and Acinetobacter spp. isolated from various non-repetitive clinical samples during the study period, were subjected to antibiotic susceptibility testing using MicroScan ID/AST system. Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry was used to confirm identity of these isolates. Additional colistin susceptibility testing of all test isolates was performed using Mikrolatest minimum inhibitory concentration antibiotic susceptibility testing kit (reference method), which is based on broth micro dilution (BMD) principle.

Statistical Analysis Used

Fisher's exact test.

Results

11.8% (4/34) of the test isolates (100% [2/2] Acinetobacter junii, 10% [1/10] E. coli and 14.3% [1/7] P. aeruginosa respectively) exhibited in vitro colistin resistance by BMD method. Categorical agreement between MicroScan ID/AST system and Mikrolatest kit w. r. t in vitro colistin susceptibility test results was as follows: 71.4% (Acinetobacter baumannii), 85.7% (P. aeruginosa) and 100% (A. junii, A. johnsonii, E. coli and Klebsiella pneumoniae), respectively. Two major errors (MEs) for A. baumannii and one very ME for P. aeruginosa respectively were observed.

Conclusions

Data generated by this study will be of help to the clinicians who are often faced with the dilemma of treating multi drug resistant infections with limited treatment options.

Raw meat-based diets for companion animals: a potential source of transmission of pathogenic and antimicrobial-resistant Enterobacteriaceae

Feeding pets raw meat-based diets (RMBDs) has become increasingly popular but may constitute a risk due to the contamination with pathogenic and antimicrobial-resistant (AMR) bacteria. The aim of this study was to evaluate commercially available RMBDs with regard to microbiological quality and occurrence of AMR Enterobacteriaceae. Of 51 RMBD samples, 72.5% did not meet the microbiological standards for Enterobacteriaceae set out by EU regulations for animal by-products intended for pet food. Furthermore, Salmonella was detected in 3.9% of the samples. AMR bacteria were found in 62.7% of the samples, the majority thereof were resistant to third-generation cephalosporins due to the production of extended-spectrum β-lactamases (ESBLs) including CTX-M-1, which is widespread in livestock, and CTX-M-15, which is the most common ESBL variant worldwide. Colistin- and aminoglycoside-resistant isolates, producing MCR-1 and RMTB, were identified in 3.9 and 2% of the samples, respectively. The majority of the AMR Escherichia coli belonged to commensal groups A or B1 and were associated with clonal complexes CC155 and CC10. Two belonged to the emerging extraintestinal pathogenic CC648, and one to the globally disseminated uropathogenic E. coli sequence type ST69, suggesting zoonotic potential. The microbiological quality and the high prevalence of AMR producing Enterobacteriaceae in RMBDs raise concerns for animal and public health.

The presence of colistin resistance gene mcr-1 and -3 in ESBL producing Escherichia coli isolated from food in Ho Chi Minh City, Vietnam

Colistin is indicated for the treatment of multidrug-resistant gram-negative bacterial infections. However, the spread of colistin-resistant bacteria harbouring an mcr gene has become a serious concern. This study investigated local foods in Vietnam for contamination with colistin-resistant bacteria. A total of 261 extended-spectrum β-lactamase (ESBL)- and AmpC-producing Escherichia coli isolates from 330 meat and seafood products were analysed for colistin susceptibility and the presence of mcr genes. Approximately, 24% (62/261) of ESBL- or AmpC-producing E. coli isolates showed colistin resistance; 97% (60/62) of colistin-resistant isolates harboured mcr-1, whereas 3% (2/62) harboured mcr-3. As the result of plasmid analysis of two strains, both plasmids harbouring mcr-3 revealed that plasmid replicon type was IncFII. Sequencing analysis indicated that an insertion sequence was present near mcr-3, suggesting that IncFII plasmids harbouring mcr-3 could be transferred to other bacterial species by horizontal transfer of the plasmid or transfer with some insertion sequence. In conclusion, ESBL-producing E. coli and AmpC-producing E. coli have acquired colistin resistance because 24% of such isolates show colistin resistance and 3% of the colistin-resistant strains harbour mcr-3. We reported the present of the mcr-3-carrying ESBL-producing E. coli isolated from pork in Vietnam.