Development and Validation of a Clinical Laboratory Improvement Amendments-Compliant Multiplex Real-Time PCR Assay for Detection of mcr Genes

Carbapenem-Resistant and Extended-Spectrum β-Lactamase-Producing Enterobacterales in Children, United States, 2016-2020

2019–2020 at 6 US sites. Among 159 CRE cases in children (median age 5 years), CRE was isolated from urine for 131 (82.4%) and blood from 20 (12.6%). Annual CRE incidence rate (cases/100,000 population) was 0.47–0.87. Among 207 ESBL-E cases in children (median age 6 years), ESBL-E was isolated from urine of 196 (94.7%) and blood of 8 (3.9%). Annual ESBL-E incidence rate was 26.5 in 2019 and 19.63 in 2020. CRE and ESBL-E rates were >2-fold higher among infants than other age groups. Most CRE and ESBL-E cases were healthcare-associated community-onset (68 [43.0%] for CRE vs. 40 [23.7%] for ESBL-E) or community-associated (43 [27.2%] for CRE vs. 109 [64.5%] for ESBL-E). Programs to detect, prevent, and treat multidrug-resistant infections must include pediatric populations (particularly the youngest) and outpatient settings.

Carbapenem-Resistant enterobacterales in individuals with and without health care risk factors -Emerging infections program, United States, 2012-2015

BACKGROUND

Carbapenem-resistant Enterobacterales (CRE) are usually healthcare-associated but are also emerging in the community.

METHODS

Active, population-based surveillance was conducted to identify case-patients with cultures positive for Enterobacterales not susceptible to a carbapenem (excluding ertapenem) and resistant to all third-generation cephalosporins tested at 8 US sites from January 2012 to December 2015. Medical records were used to classify cases as health care-associated, or as community-associated (CA) if a patient had no known health care risk factors and a culture was collected <3 days after hospital admission. Enterobacterales isolates from selected cases were submitted to CDC for whole genome sequencing.

RESULTS

We identified 1499 CRE cases in 1194 case-patients; 149 cases (10%) in 139 case-patients were CA. The incidence of CRE cases per 100,000 population was 2.96 (95% CI: 2.81, 3.11) overall and 0.29 (95% CI: 0.25, 0.35) for CA-CRE. Most CA-CRE cases were in White persons (73%), females (84%) and identified from urine cultures (98%). Among the 12 sequenced CA-CRE isolates, 5 (42%) harbored a carbapenemase gene.

CONCLUSIONS

Ten percent of CRE cases were CA; some isolates from CA-CRE cases harbored carbapenemase genes. Continued CRE surveillance in the community is critical to monitor emergence outside of traditional health care settings.

Molecular Epidemiology of mcr-1-Positive Escherichia coli and Klebsiella pneumoniae Isolates: Results from Russian Sentinel Surveillance (2013-2018)

BACKGROUND

The dissemination of mobile colistin resistance (mcr) genes is a serious healthcare threat because polymyxins represent "last-line" therapeutics for multi-drug-resistant Gram-negative pathogens. This study aimed to assess the prevalence of colistin resistance and mcr genes and characteristics of clinical Escherichia coli (Eco) and Klebsiella pneumoniae (Kpn) isolates and plasmids carrying these genes in Russia.

METHODS

A total of 4324 Eco and 4530 Kpn collected in the frame of sentinel surveillance in 2013-2018 were tested for susceptibility to colistin and other antibiotics using the broth microdilution method. mcr genes were screened by real-time PCR. Phylogeny, genomic features and plasmids of mcr-positive isolates were assessed using whole-genome sequencing and subsequent bioinformatic analysis.

RESULTS

Colistin resistance was detected in 2.24% Eco and 9.3% Kpn. Twenty-two (0.51%) Eco and two (0.04%) Kpn from distant sites carried mcr-1.1. Most mcr-positive isolates co-harbored ESBLs and other resistance determinants to various antibiotic classes. The mcr-positive Eco belonged to 16 MLST types, with ST359 being most common; Kpn belonged to ST307 and ST23. mcr-1.1 was carried mainly in IncI2 (n = 18) and IncX4 (n = 5) plasmids highly similar to those identified previously in human, animal and environmental isolates.

CONCLUSION

This study demonstrated a dissemination of "typical" mcr-bearing plasmids among diverse Eco and Kpn genotypes and across a wide geographic area in Russia. Given the frequent association of mcr with other resistance determinants and potential clinical impact, the continual surveillance of this threat is warranted.

Global Prevalence and Molecular Epidemiology of mcr-Mediated Colistin Resistance in Escherichia coli Clinical Isolates: A Systematic Review

BACKGROUND AND AIM

The continuing rise in infections caused by multi-drug resistant (MDR) bacteria is one of the most serious public health issues in today's societies. Colistin is a last-resort antimicrobial medication used to treat infections caused by MDR gram-negative bacteria; therefore resistance to this antibiotic is extremely hazardous. The current study aimed to evaluate the global prevalence and distribution of colistin resistance genes among human clinical isolates of Escherichia coli (E. coli) as a systematic review.

METHODS

PubMed, Embase, and Web of Science databases were systematically searched. For further evaluation, all original English-language articles that demonstrated colistin resistance in E. coli clinical isolates published between 2000 and 2020 were examined.

RESULTS

Out of 4857 initial articles, after various stages of review and evaluation, 190 related articles were selected. More than 79 % of the publications selected in this research were published from 2014 to 2020. In Asia, Europe, America, Africa, and Oceania, the prevalence of mobilized colistin resistance (mcr) producing colistin-resistant E. coli was 66.72%, 25.48%, 5.19%, 2.27%, and 0.32 %, respectively.

CONCLUSION

The recent widespread spreading of E. coli strains harboring mcr conferring colistin resistance, especially in Asia and Europe, is concerning and needs more attention.

Novel Quadruplex PCR for detecting and genotyping mobile colistin resistance genes in human samples

Since 2016, several mobile colistin resistance (mcr) genes have been identified worldwide. It's worth noting that only mcr-1, mcr-3, mcr-8, and mcr-10 have been reported isolated directly from clinical samples which created greater risk to human health than other mcr gene types. A novel Quadruplex polymerase chain reaction (Quad-PCR) protocol was developed to detect and genotype transferable colistin-resistance genes (mcr-1, mcr-3, mcr-8, mcr-10) in Enterobacteria for clinical laboratory purposes. The protocol was validated by testing 11 clinical isolates of Escherichia coli and 3 clinical isolates of Klebsiella of human origin, each well characterized and prospectively validated. The Quad-PCR assay showed full concordance with whole-genome sequence data and displayed higher sensitivity and 100% specificity. The Quad-PCR assay achieved genotyping of mcr alleles (as singleton and mixture with double or triple gene types) described in one test.

Rapid and Sensitive Detection of the Colistin Resistance Gene mcr-3 by Loop-Mediated Isothermal Amplification and Visual Inspection

Objective: The distribution of colistin resistance in mcr-carrying bacteria poses a threat to global public health. In particular, the newly identified mcr-3 allele has spread globally, especially in China, second only to mcr-1. In this study, we aimed to develop a loop-mediated isothermal amplification (LAMP) assay for rapid, sensitive, and visual detection of the presence of the mcr-3 gene. Materials and Methods: A total of 13 clinical bacterial strains and 11 negative strains were used in this study. We designed LAMP Primers, optimized reaction conditions, used three different methods to detect LAMP amplification products: (1) agarose gel electrophoresis, (2) LAMP-hydroxy naphthol blue (HNB) detection, (3) LAMP-SYBR Green I (LAMP-SGI) visual inspection, and evaluated its specificity and sensitivity. Results: The amplification reaction was completed in 1 hr at 62°C under isothermal conditions. The final optimized mixtures contained 100 mM KCl, 100 mM (NH₄)₂SO₄, 20 mM MgSO₄, 1% Triton X-100, 1.2 μL HNB, and 0.5 μL SYBR Green I as additives to the initial reaction mixture. LAMP detection, including two visual methods, LAMP-HNB and LAMP-SGI, of mcr-3 possessed the same specificity and a 10-fold higher sensitivity compared with a conventional polymerase chain reaction assay using the same samples. Conclusion: We successfully established an mcr-3 LAMP detection with portability and rapidity of the reaction by the easily distinguishable color changes in the reaction tubes. This visual LAMP assay for mcr-3 detection was simple, time saving, and economical, especially suited to field laboratories.

Current and emerging polymyxin resistance diagnostics: A systematic review of established and novel detection methods

The emergence of polymyxin resistance, due to transferable mcr genes, threatens public and animal health as there are limited therapeutic options. As polymyxin is one of the last-line antibiotics, there is a need to contain the spread of its resistance to conserve its efficacy. Herein, we describe current and emerging polymyxin resistance diagnostics to inform faster clinical diagnostic choices. A literature search in diverse databases for studies published between 2016 and 2020 was performed. English articles evaluating colistin resistance methods/diagnostics were included. Screening resulted in the inclusion of 93 journal articles. Current colistin resistance diagnostics are either phenotypic or molecular. Broth microdilution is currently the only gold standard for determining colistin MICs (minimum inhibitory concentration). Phenotypic methods comprise of agar-based methods such as CHROMagar™ Col-APSE, SuperPolymyxin, ChromID^® Colistin R, LBJMR and LB medium; manual MIC-determiners viz., UMIC, MICRONAUT MIC-Strip and ComASP Colistin; automated antimicrobial susceptibility testing systems such as BD Phoenix, MICRONAUT-S, MicroScan, Sensititre and Vitek 2; MCR-detectors such as lateral flow immunoassay (LFI) and chelator-based assays including EDTA- and DPA-based tests, that is, combined disk test, modified colistin broth-disk elution (CBDE), Colispot, and Colistin MAC test as well as biochemical colorimetric tests, that is, Rapid Polymyxin NP test and Rapid ResaPolymyxin NP test. Molecular methods only characterize mobile colistin resistance; they include PCR, LAMP and whole-genome sequencing. Due to the faster turnaround time (≤3 h), improved sensitivity (84%-100%) and specificity (93.3%-100%) of the Rapid ResaPolymyxin NP test and Fastinov^® , we recommend this test for initial screening of colistin-resistant isolates. This can be followed by CBDE with EDTA or the LFI as they both have 100% sensitivity and a specificity of ≥94.3% for the rapid screening of mcr genes. However, molecular assays such as LAMP and PCR may be considered in well-equipped clinical laboratories.

Rapid detection of human origin colistin-resistance genes mcr-1, mcr-3, mcr-8, mcr-10 in clinical fecal samples

Plasmid-mediated colistin-resistance genes have been reported in human origin clinical samples worldwide which raises its threats to human infections. Notably, mcr-1, mcr-3, mcr-8, and mcr-10 have been reported isolated directly from clinical samples which creates more seriously threaten to human health than other mcr gene types. A multiplex polymerase chain reaction (Multi-PCR) protocol was developed to detect and genotype mobile colistin-resistance genes (mcr-1, mcr-3, mcr-8, mcr-10) in Enterobacteria for clinical laboratory purposes. We first designed four pairs of new primers for the amplification of mcr-1, mcr-3, mcr-8, and mcr-10 gene respectively to achieve stepwise separation of amplicons between 216 and 241 bp, and complete this Multi-PCR system with the assistance of another pair of universal primer. Among which the forward primers for mcr-8 and mcr-10 amplicons were identical. The protocol was validated by testing 11 clinical isolates of Escherichia coli and 3 clinical isolates of Klebsiella from human origin, each well characterized and prospectively validated. The Multi-PCR assay showed full concordance with whole-genome sequence data and displayed higher sensitivity and 100% specificity. The assay could detect all variants of the various mcr alleles described. The Multi-PCR assay successfully genotyped of mcr alleles described in one test.

An inventory of 44 qPCR assays using hydrolysis probes operating with a unique amplification condition for the detection and quantification of antibiotic resistance genes

Early antibiotic resistance determinants (ARDs) detection in humans or animals is crucial to counteract their propagation. The ARDs quantification is fundamental to understand the perturbation caused by disruptors, such as antibiotics, during therapies. Forty-three qPCRs on the most diffused ARDs and integrons among human and animal Enterobacterales, and one on the 16S rDNA for bacteria quantification, were developed. The qPCRs, using hydrolysis probes, operated with a unique amplification condition and were tested analytically and diagnostically performing 435 reactions on five positive and negative controls for each qPCR. Diagnostic sensitivity and specificity were confirmed by PCR and genome sequencing of control isolates, demonstrating 100% performance for all qPCRs. An easy and rapid discrimination method for the epidemiologically relevant bla_CTX-Ms is provided. This large, noncommercial qPCRs inventory could serve for precise quantification of ARDs, but also as a rapid screening tool for surveillance purposes, providing the basis for further high-throughput developments.

Prevalence and Molecular Typing of Colistin-Resistant Pseudomonas aeruginosa (CRPA) Among β-Lactamase-Producing Isolates: A Study Based on High-Resolution Melting Curve Analysis Method

Background

The frequency and production of β-lactamase enzymes may be different in colistin-resistant Pseudomonas aeruginosa (CRPA) strains compared to susceptible strains. The purpose of this study was to investigate the relationship between colistin resistance and β-lactamase enzymes in different Sequence Types (ST) of P. aeruginosa.

Methods

A total of 101 P. aeruginosa isolates were collected from different samples. The antimicrobial susceptibilities of the bacterial isolates were examined by disk diffusion and MIC E-test methods. Also, real-time PCR and high-resolution melting curve analysis (HRMA) assay were performed to detect the resistance genes.

Results

Out of the 101 P. aeruginosa isolates, four isolates (3.96%) were resistant to colistin. Also, 39 isolates (38.61%) were considered as MDR, and eight isolates (7.92%) were considered as XDR. Further, 25 (24.75%) and 26 isolates (25.74%) were produced ESBL and carbapenemase enzymes, respectively. According to HRMA results, four isolates (3.96%) were positive for pmrA, three isolates (2.97%) were positive for mcr-1, 25 isolates (24.75%) were positive for blaTEM, 24 isolates (23.76%) were positive for blaSHV, 26 isolates (25.75%) were positive for blaKPC, and 23 isolates (22.77%) were positive for blaIMP genes. Furthermore, ST108 and ST250 showed the highest distribution in P. aeruginosa isolates. Also, ST217, ST1078, and ST3340 were reported as novel types in CRPA strains.

Conclusion

Concerns about the prevalence of CRPA strains should be taken seriously. Also, our results showed that the mcr-1 gene plays a vital role in the distribution of ESBL and KPC-producing P. aeruginosa strains.

New approach to identify colistin-resistant Pseudomonas aeruginosa by high-resolution melting curve analysis assay

Colistin-resistant Pseudomonas aeruginosa (CRPA), as a health care system threat, is increasing globally. This study aimed was to determine CRPA by high-resolution melting curve (HRM) analysis method. The HRM method was done on standard strains of P. aeruginosa and CRPA strains. Ninefold serial dilutions of known genomic DNA (gDNA) and plasmid DNA (pDNA) concentrations, extracted from P. aeruginosa NCTC13715 and P. aeruginosa NCTC10728 were prepared and tested by melting curve analysis and HRM assay. Data analysis was performed using the Step-One Plus Software v2.3 and hrm Software v3.0.1. The results of the melt curve analysis and HRM showed a very similar melt peak for all positive controls with a melt temperature that ranged from 88·1°C to 88·6°C for the 16srRNA, 90·0°C to 90·05°C for the mcr-1 and 91·2°C to 91·7°C for the pmrA gene. Furthermore, the data indicated that the HRM approach has the sensitivity to detect 10⁰  CFU per ml for the 16srRNA gene, 10¹  CFU per ml for the pmrA gene, and 10³  CFU per ml for the mcr-1 gene. According to our findings, it was concluded that the HRM method could detect 10⁰ to 10³  CFU per ml of P. aeruginosa gDNA and pDNA. Therefore, CRPA strains can be identified with high sensitivity and specificity by HRM assay. SIGNIFICANCE AND IMPACT OF THE STUDY: The highlight of our research is about the detection of bacteria resistance genes to antibiotics by advanced molecular methods, which means high-resolution melting curve (HRM) analysis. We determined that the HRM method in identifying colistin-resistant P. aeruginosa has high accuracy and speed, and with high sensitivity and specificity.

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.

Evaluation of the MicroScan Colistin Well and Gradient Diffusion Strips for Colistin Susceptibility Testing in Enterobacteriaceae

Many laboratories are unable to perform colistin susceptibility testing. Diffusion-based antimicrobial susceptibility testing methods are not recommended, and not all laboratories have the capacity to perform broth microdilution (BMD). Using a multistep tiered approach, we investigated whether the adapted use of the MicroScan colistin well (4 μg/ml) could enhance laboratory capacity for the detection and subsequent molecular characterization of colistin-resistant Enterobacteriaceae For the MicroScan colistin well, categorical agreement with BMD was 92.7%, and the very major error rate was 10.7%. For gradient diffusion strips, the categorical agreement was 86.4%, and the very major error rate was 53.6%. The MicroScan colistin well detected all isolates carrying mcr-1 or mcr-2 genes (n = 16), but gradient diffusion strips identified an MIC of ≥4 for colistin for only 62.5% of these isolates. A 6-month prospective phenotypic and genotypic study performed at a single clinical microbiology laboratory assessed isolates growing in the MicroScan colistin well for concordance. While 37 of 39 isolates growing in the MicroScan colistin well displayed a colistin MIC of ≥4 by BMD, all were determined to be negative for the mcr-1 and mcr-2 genes by PCR. A retrospective review of all Escherichia coli, Klebsiella spp., and Enterobacter spp. tested by MicroScan at this laboratory in 2016 identified 260 of 7,894 (3.3%) isolates that grew in the MicroScan colistin well. Based on the data presented, clinical and public health laboratories could use the MicroScan colistin well as a first screen for the detection of isolates displaying elevated colistin MICs, which could then undergo further characterization.