Assessment of two selective agar media to isolate colistin-resistant bovine Escherichia coli: Correlation with minimal inhibitory concentration and presence of mcr genes

Characterization of antibiotic resistance genes and bacteria in a municipal water resource recovery facility

Municipal water resource recovery facilities (WRRFs) are important sources of antibiotic-resistant bacteria and genes (ARB and ARGs). In this study, antibiotic-resistant total heterotrophic bacteria (THB_R ) counts (CFU/ml) cultivated from influent, effluent of activated sludge process, and outflow of disinfection unit of an urban WRRF were investigated for the presence of 16, 32, 64, and 128 μg/ml of nine antibiotics. The isolates of Pseudomonas spp., Acinetobacter spp., and Escherichia coli obtained from effluent of activated sludge process were subjected for molecular identification by detecting the 16S rRNA gene sequences. Additionally, using the polymerase chain reaction method (PCR), the isolates were investigated for the presence of bla_SHV , bla_TEM , bla_CTX-M , bla_VIM , sul1, and qnrS genes. According to the results, the abundance of THB_R counts was not significantly reduced by the biological treatment except for cefixime and sulfamethoxazole; it also increased for some antibiotics after disinfection unit. The average removal efficiency of THB_R resistant to ciprofloxacin, sulfamethoxazole, and ceftazidime were 7.9 ± 1.7%, 41.8 ± 2.1%, and 14.4 ± 6.2%, respectively. Also, all the tested isolates were resistant to at least four antibiotics. For all antibiotics, the resistance ratio (THB_R /THB) significantly increased in the effluent and after chlorination unit. Among 12 resistant isolates, bla_TEM and sul1 genes were the most frequently detected ones involved in 92% and 83% of the isolates, respectively. Both bla_TEM and sul1 genes were found in 100% of E. coli, and 83% and 67% of Pseudomonas spp. isolates, respectively. Further efforts are necessary to limit the transmission of ARB and ARGs from WRRFs into the environment and prevent human health threats. PRACTITIONER POINTS: The ratio of resistance significantly increased after biological treatment. Up to 40% of heterotrophic bacteria in the effluent was antibiotic resistant. bla_TEM and sul1 genes were more prevalent (92%) in all isolates of bacteria. Both bla_TEM and sul1 genes were found in 100% of E. coli isolates. Pseudomonas spp. holds bla_TEM and sul1 genes in 83% and 67% of isolates, respectively.

In Vitro and In Vivo Assessments of Two Newly Isolated Bacteriophages against an ST13 Urinary Tract Infection Klebsiella pneumoniae

Antibiotic resistance represents a major public health concern requiring new alternatives including phage therapy. Klebsiella pneumoniae belongs to the ESKAPE bacteria and can cause urinary tract infections (UTIs). The aims of this study were to isolate and characterize new bacteriophages against a K. pneumoniae strain isolated from UTIs and to assess their efficacy in vitro and in vivo in a Galleria (G.) mellonella larvae model. For this purpose, two bacteriophages were newly isolated against an ST13 K. pneumoniae strain isolated from a UTI and identified as K3 capsular types by wzi gene PCR. Genomic analysis showed that these bacteriophages, named vB_KpnP_K3-ULINTkp1 and vB_KpnP_K3-ULINTkp2, belong to the Drulisvirus genus. Bacteriophage vB_KpnP_K3-ULINTkp1 had the narrowest host spectrum (targeting only K3), while vB_KpnP_K3-ULINTkp2 also infected other Klebsiella types. Short adsorption times and latent periods were observed for both bacteriophages. In vivo experiments showed their ability to replicate in G. mellonella larvae and to decrease host bacterial titers. Moreover, both bacteriophages improved the survival of the infected larvae. In conclusion, these two bacteriophages had different in vitro properties and showed in vivo efficacy in a G. mellonella model with a better efficiency for vB_KpnP_K3-ULINTkp2.

Establishment of Epidemiological Resistance Cut-Off Values of Aquatic Aeromonas to Eight Antimicrobial Agents

The abuse of antibiotics in aquaculture has led to the increasing rate of antibiotic resistance of aquatic bacteria including Aeromonas, which is an increasing threat to environmental and human health. To date, no epidemiological cut-off values (COWT) for Aeromonas spp. have been established by the Clinical and Laboratory Standards Institute nor the European Commission on Antimicrobial Susceptibility Testing. In this study, commercially prepared minimum inhibitory concentration (MIC) test 96-well plates (dry-form plates) were used to determine the MIC of eight antimicrobial agents against 556 Aeromonas strains. The obtained MIC distributions were simulated and analyzed by NRI and ECOFFinder to obtain tentative COWT values for Aeromonas spp. The COWT values of eight kinds of representative antimicrobial agents including trimethoprim–sulfamethoxazole, erythromycin, doxycycline, neomycin, colistin, florfenicol, enrofloxacin, and ceftazidime for Aeromonas spp. were established and were 0.25, 64/32, 4/2, 8, 4, 1, 0.062/0.125, and 0.5 μg/mL, respectively. Results showed that Aeromonas spp. had a very high proportion of non-wild-type strains to enrofloxacin, florfenicol, and doxycycline, which are the most widely used antimicrobials in aquaculture. The COWT values for Aeromonas spp. obtained in this study can contribute to the final establishment of COWT for Aeromonas spp. internationally.

Colistin Resistant mcr Genes Prevalence in Livestock Animals (Swine, Bovine, Poultry) from a Multinational Perspective. A Systematic Review

The objective of this review is to collect and present the results of relevant studies on an international level, on the subject of colistin resistance due to mcr genes prevalence in livestock animals. After a literature search, and using PRISMA guidelines principles, a total of 40 swine, 16 bovine and 31 poultry studies were collected concerning mcr-1 gene; five swine, three bovine and three poultry studies referred to mcr-2 gene; eight swine, one bovine, two poultry studies were about mcr-3 gene; six swine, one bovine and one poultry manuscript studied mcr-4 gene; five swine manuscripts studied mcr-5 gene; one swine manuscript was about mcr-6, mcr-7, mcr-8, mcr-9 genes and one poultry study about mcr-10 gene was found. Information about colistin resistance in bacteria derived from animals and animal product foods is still considered limited and that should be continually enhanced; most of the information about clinical isolates are relative to enteropathogens Escherichia coli and Salmonella spp. This review demonstrates the widespread dispersion of mcr genes to livestock animals, indicating the need to further increase measures to control this important threat for public health issue.

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.

How to: screening for mcr-mediated resistance to colistin

BACKGROUND

Colistin belongs to the last-resort antibiotics. The discovery of plasmid-bound colistin resistance mediated by the mcr-gene(s) is of great concern because, given its biological potential, there is a risk of its rapid spread.

OBJECTIVES

To discuss the current literature on the methods for the screening for mcr-mediated resistance to colistin.

SOURCES

Literature was drawn from a search of PubMed from 1 January 2016 to 26 April 2021.

CONTENT

The selective culture-based or culture-independent approach can be used for the screening of mcr-mediated resistance to colistin in clinical samples. Rapid Polymyxin NP, Colistin Drop or Colistin Agar Spot tests are applicable for the selection of isolates with a suspected resistance to colistin that has to be confirmed by broth microdilution. The mcr-mediated resistance to colistin can be confirmed by the detection of the causal gene(s) or by phenotype using EDTA-colistin broth disc elution; production of the MCR-1 enzyme can be confirmed with lateral flow immunoassay, using matrix-assisted laser desorption/ionization time-of flight or liquid chromatography-based mass spectrometry. Whole-genome sequencing (WGS) is the ultimate typing method. When a WGS platform is not available at a healthcare facility, a WGS-outsourced service, in combination with freely available bioinformatics tools, allows for the characterization of the mcr-gene(s) carrying isolates.

IMPLICATIONS

mcr-mediated colistin resistance should be monitored through active targeted screening. The broth microdilution method is required for colistin susceptibility testing but as only a selected number of clinical isolates are tested, colistin resistance, including mcr-mediated, may remain undetected. In mcr-1-positive Escherichia coli isolates, the MIC to colistin can range from 2 to 8 mg/L, so it is proposed that Enterobacterales with a colistin MIC of 2 mg/L should also be included in the mcr-mediated colistin resistance screening and those with a confirmed mcr-genotype and/or MCR-phenotype should be considered to be colistin-resistant.

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.

Bacteria Broadly-Resistant to Last Resort Antibiotics Detected in Commercial Chicken Farms

Resistance to last resort antibiotics in bacteria is an emerging threat to human and animal health. It is important to identify the source of these antimicrobial resistant (AMR) bacteria that are resistant to clinically important antibiotics and evaluate their potential transfer among bacteria. The objectives of this study were to (i) detect bacteria resistant to colistin, carbapenems, and β-lactams in commercial poultry farms, (ii) characterize phylogenetic and virulence markers of E. coli isolates to potentiate virulence risk, and (iii) assess potential transfer of AMR from these isolates via conjugation. Ceca contents from laying hens from conventional cage (CC) and cage-free (CF) farms at three maturity stages were randomly sampled and screened for extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, carbapenem-resistant Acinetobacter (CRA), and colistin resistant Escherichia coli (CRE) using CHROMagar™ selective media. We found a wide-spread abundance of CRE in both CC and CF hens across all three maturity stages. Extraintestinal pathogenic Escherichia coli phylogenetic groups B2 and D, as well as plasmidic virulence markers iss and iutA, were widely associated with AMR E. coli isolates. ESBL-producing Enterobacteriaceae were uniquely detected in the early lay period of both CC and CF, while multidrug resistant (MDR) Acinetobacter were found in peak and late lay periods of both CC and CF. CRA was detected in CF hens only. bla_CMY was detected in ESBL-producing E. coli in CC and CF and MDR Acinetobacter spp. in CC. Finally, the bla_CMY was shown to be transferrable via an IncK/B plasmid in CC. The presence of MDR to the last-resort antibiotics that are transferable between bacteria in food-producing animals is alarming and warrants studies to develop strategies for their mitigation in the environment.

Comparative Evaluation of CHROMagar COL-APSE, MicroScan Walkaway, ComASP Colistin, and Colistin MAC Test in Detecting Colistin-resistant Gram-Negative Bacteria

Colistin has become a critical antibiotic for fatal Gram-negative infections owing to the proliferation of multidrug-resistant carbapenemase-producing bacteria. Thus, cheaper, faster, efficient and easier-to-use colistin diagnostics are required for clinical surveillance, diagnoses and therapeutics. The sensitivity, specificity, major error (ME), very major error (VME), categorial agreement, essential agreement, turnaround time (TAT), average cost, and required skill for four colistin resistance diagnostics viz., CHROMagar COL-APSE, ComASP Colistin, MicroScan, and Colistin MAC Test (CMT) were evaluated against broth microdilution (BMD) using 84 Gram-negative bacterial isolates. A multiplex PCR (M-PCR) was used to screen all isolates to detect the presence of the mcr-1 to mcr-5 genes. A 15-point grading scale was used to grade the tests under skill, ease, processing time etc. mcr-1 was detected by both M-PCR and CMT in a single E. coli isolate, with other PCR amplicons suggestive of mcr-2, -3 and -4 genes being also observed on the gel. The sensitivity and specificity of CHROMagar COL-APSE, MicroScan, and ComASP Colistin, were 82.05% and 66.67%, 92.31% and 76.92%, and 100% and 88.89% respectively. The MicroScan was the most expensive at a cost (per sampe tested) of R221.6 ($15.0), followed by CHROMagar COL-APSE (R118.3; $8.0), M-PCR (R75.1; $5.1), CMT (R20.1; $1.4) and ComASP Colistin (R2.64; $0.2). CHROMagar was the easiest to perform, followed by ComASP Colistin, M-PCR, MicroScan, CMT and BMD whilst M-PCR and MicroScan required higher skill. The ComASP Colistin was the best performing diagnostic test, with low VME and ME, making it recommendable for routine colistin sensitivity testing in clinical laboratories; particularly, in poorer settings. It is however limited by a TAT of 18-24 hours.