Evaluation of the BD Phoenix M50 Automated Microbiology System for Antimicrobial Susceptibility Testing with Clinical Isolates in Korea

Assessment of in vitro colistin susceptibility of carbapenem-resistant clinical Gram-negative bacterial isolates using four commercially available systems & Whole-genome sequencing: A diagnostic accuracy study

AIM

To analyze the diagnostic utility of commercially available platforms and Whole-genome sequencing (WGS) for accurate determination of colistin susceptibility test results.

MATERIAL & METHODS

An exploratory diagnostic accuracy study was conducted in which sixty carbapenem-resistant Gram-negative bacteria were subjected to identification and AST using MALDI-TOF MS & MicroScan walkaway 96 Plus. Additional AST was performed using the BD Phoenix system and Mikrolatest colistin kit. The test isolates were subjected to Vitek-2 and WGS at CRL, Bengaluru.

RESULTS

There was no statistically significant agreement between the colistin susceptibility results obtained by WGS, with those of commercial phenotypic platforms. The MicroScan 96 Plus had the highest sensitivity (31 %) & NPV (77 %), and the BD Phoenix system had the highest specificity (97 %) and PPV (50 %), respectively, for determining colistin resistance.

CONCLUSION

The utility of WGS as a tool in AMR surveillance and validation of phenotypic AST methods should be explored further.

Prevalence, antibiotic resistance profile, MBLs encoding genes, and biofilm formation among clinical carbapenem-resistant Enterobacterales isolated from patients in Mohammed VI University Hospital Centre, Morocco

Enterobacterales are frequently a major cause of human infections. The emergence of carbapenem resistance as well as the biofilm formation complicate their management. In this regard, this study aimed to investigate the prevalence, antibiogram, carbapenemase genes, and biofilm production among Enterobacterales. For this purpose, 18 172 clinical specimens from hospitalized patients at Mohammed VI University Hospital were collected over two years (2018-2019). The bacteriological investigation was performed to isolate Enterobacterales. Subsequently, BD-Phoenix and MALDI-TOF-MS were used for bacterial identification. The production of ESBLs and carbapenemases was assessed using phenotypic tests and PCR. The biofilm formation was eventually carried out. Out of 195 carbapenem-resistant Enterobacterales strains, 190 were carbapenemase producers, and 74 Enterobacterales produced metallo-beta-lactamases (MBLs). The PCR results revealed that blaNDM was the most common carbapenemase gene, present in 62 cases, followed by the co-existence of blaNDM and blaOXA-48 in 12 cases. Klebsiella pneumoniae was the most frequently identified species among the 74 New Delhi metallo-β-lactamase (NDM) isolates and the XDR resistance phenotype was the most prevalent with 58.10%. Additionally, all 74 NDM-positive Enterobacterales were able to form biofilms, with 82.4% being strong producers. This study highlights the need for rapid detection of carbapenemase and biofilm production in our hospital to manage this health concern.

Extension of bacterial rDNA sequencing for simultaneous methylation detection and its application in microflora analysis

Although polymerase chain reaction (PCR) amplification and sequencing of the bacterial 16S rDNA region has numerous scientific applications, it does not provide DNA methylation information. Herein, we propose a simple extension for bisulfite sequencing to investigate 5-methylcytosine residues in the bacterial 16S rDNA region from clinical isolates or flora. Multiple displacement amplification without DNA denaturation was used to preferentially pre-amplify single-stranded bacterial DNA after bisulfite conversion. Following the pre-amplification, the 16S rDNA region was analyzed using nested bisulfite PCR and sequencing, enabling the simultaneous identification of DNA methylation status and sequence data. We used this approach (termed sm16S rDNA PCR/sequencing) to identify novel methylation sites and a methyltransferase (M. MmnI) in Morganella morganii and different methylation motifs among Enterococcus faecalis strains from small volumes of clinical specimens. Further, our analysis suggested that M. MmnI may be correlated to erythromycin resistance. Thus, sm16S rDNA PCR/sequencing is a useful extension method for analyzing the DNA methylation of 16S rDNA regions in a microflora, providing additional information not provided by conventional PCR. Given the relationship between DNA methylation status and drug resistance in bacteria, we believe this technique can be effectively applied in clinical sample testing.

Evaluation of sulbactam and colistin/sulbactam efficacy against multiple resistant Acinetobacter baumannii blood isolates

PURPOSE

We aimed to compare the results of the BD Phoenix (TM) M50 ID/AST system and the gold standard broth microdilution method. We also evaluated the potential of a new therapeutic combination (colistin/sulbactam) for colistin resistance among Acinetobacter baumanni strains.

METHODS

Growth in blood samples was detected with the BACTEC (BD Becton Dickinson, ABD) continuous monitoring blood culture system. Strains were identified by Phoenix (BD Phoenix™ M50, ABD) automated bacterial identification system and antimicrobial susceptibility results were obtained. A total of 92 A. baumannii complex isolates showing resistance to at least three antibiotic classes were included in the study. Colistin susceptibility results (both susceptible and resistant strains) detected by the Phoenix device were confirmed by the reference method, the liquid microdilution method. The concentration index (FIC) was used to determine the efficacy of fractional inhibitor drug combinations, the efficacy of colistin/sulbactam combination against 50 multiresistant A. baumannii complex strains was investigated using the checkerboard method.

RESULTS

10 (10.9%) of 92 isolates were resistant to colistin and 80 (86.9%) to sulbactam. With the automation system, only 2 of 10 isolates were found resistant to colistin, while 8 isolates were susceptible. For this reason, the very major error rate of the Phoenix M50 automatic system among resistant isolates was determined as 8/10. It was determined that 6 (12%) of the colistin/sulbactam combination had a synergistic effect and 44 (88%) had an additive interaction. No antagonistic interaction was detected with the colistin-sulbactam combination in this study.

CONCLUSION

A. baumannii strains should be confirmed by the broth microdilution method, which is the reference method, against the MIC results detected by automated systems. It was concluded that the use of colistin alone should be avoided in the treatment of A. baumannii infections.

Performance Evaluation of the Quantamatrix QMAC-dRAST System for Rapid Antibiotic Susceptibility Testing Directly from Blood Cultures

Objectives: Rapid antibiotic susceptibility testing (AST) for positive blood cultures can improve patient clinical outcomes if the time to an effective antimicrobial therapy is shortened. In this study, we tested the Quantamatrix dRAST system (QMAC-dRAST), a rapid AST system based on time-lapse microscopic imagery of bacterial colony formation in agarose. Methods: Evaluation of the QMAC-dRAST was performed from 250 monobacterial blood cultures including 130 Enterobacterales, 20 non-fermentative Gram-negative bacteria, 69 staphylococci and 31 enterococci. Blood cultures were recovered from anonymous patients or from spiking experiments to enrich our study with bacterial species and resistant strains. Categorical agreement (CA), minor errors (me), major errors (ME) and very major errors (VME) were calculated in comparison to the results obtained from the BD Phoenix™ M50. Discrepancies between the Phoenix™ M50 and QMAC-dRAST results were investigated using the gradient strip method. The repeatability and reproducibility performance of the QMAC-dRAST was assessed for 16 strains, each strain being tested five times from a spiked blood culture. Results: The overall CAs for Enterobacterales, non-fermentative Gram-negative bacteria, staphylococci and enterococci were 95.1%, 91.2%, 93.4% and 94.5%, respectively. The VME percentage was below 4% for all the groups except for staphylococci, which showed a VME rate of 7%. The median time to result was 6.7 h (range: 4.7–7.9). Repeatability and reproducibility assays showed a high reliability of AST results with best and worst ratios of 98.8% and 99.6% and 95.0% and 98.3%, respectively. Conclusions: The QMAC-dRAST is a fast and reliable system to determine AST directly from monobacterial blood cultures with a major TAT reduction compared to conventional AST testing.

Comparative evaluation of two automated ID/AST systems and mikrolatest kit in assessing the In Vitro colistin susceptibility of carbapenem-resistant enterobacteriaceae isolates: A single-center exploratory study from North India

Aims:

To generate preliminary data about comparative evaluation of two automated ID/AST systems and Mikrolatest kit in determining in vitro colistin susceptibility of carbapenem-resistant Enterobacteriaceae spp.

Materials and methods:

Twenty-three carbapenem-resistant Escherichia coli and Klebsiella pneumoniae and two carbapenem-sensitive multidrug-resistant E. coli isolates obtained from various clinical samples of inpatients were included in the study. Species-level identification and antibiotic susceptibility testing (AST) of test isolates was performed using BD phoenix and MicroScan WalkAway 96 Plus automated systems. Identity was reconfirmed by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). Additional colistin susceptibility testing was performed using Mikrolatest MIC colistin susceptibility testing kit (reference method).

Results:

Results showed that 16% isolates (27.3% [3/11] K. pneumoniae and 7.1% [1/14] E. coli) exhibited in vitro colistin resistance by the reference method. While the categorical agreement between BD Phoenix M50 ID/AST system and reference test w. r. t in vitro colistin susceptibility results was 100% and 92.9% for K. pneumoniae & E. coli, respectively, it was much lower between MicroScan WalkAway 96 plus ID/AST system and the latter. Almost perfect agreement (96%; kappa: 0.834) was observed between BD Phoenix M50 system and reference method.

Conclusions:

The results of this study are preliminary and cannot be generalized. Multicentric studies with large sample sizes should be conducted throughout the country to gain a deeper understanding of the subject under consideration.

Virulence and intermediate resistance to high-end antibiotic (teicoplanin) among coagulase-negative staphylococci sourced from retail market fish

This study reports the distribution of enterotoxigenic determinants among staphylococci and the susceptibility of staphylococci to various classes of antibiotics. We observed all the isolates as resistant to beta-lactam antibiotics and a few as resistant to non-beta-lactam antibiotics such as clindamycin (47.4%), erythromycin (44.7%), gentamicin (23.7%), norfloxacin (34.2%), tetracycline (26.3%), trimethoprim-sulfamethoxazole (15.8%) etc. The resistance of S. sciuri (n = 1) and S. haemolyticus (n = 1) to rifampicin and intermediate resistance of S. gallinarum (n = 2) to teicoplanin, a high-end antibiotic, are also observed in this study. The multidrug-resistance (≥ 3 classes of antibiotics) was recorded in 23 (60.5%) isolates. The virulomes such as sea, seb, seg and sei were identified predominantly in S. haemolyticus. Surprisingly, certain isolates which were phenotypically confirmed as biofilm-producers by Congo red agar (CRA) test did not harbor biofilm-associated loci. This implies the protein-mediated mechanism of biofilm formation as an alternative to polysaccharide intercellular adhesin (PIA) in staphylococci. However, icaAD locus which encodes PIA was identified in 10 (26.3%) isolates and the eno locus, encoding elastin-binding protein which can accelerate the biofilm production, is identified in all the isolates. The possession of type V SCCmec elements by the S. haemolyticus (15.8%) raised the concern about the rapid dissemination of mecA gene to other species of staphylococci including the virulent S. aureus. In short, this study acknowledges the toxigenicity of coagulase-negative staphylococci (CoNS). Through this study, surveillance of antimicrobial resistance and transference of virulomes in staphylococci is warranted.

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.

Performance Evaluation of BD Phoenix NMIC-413 Antimicrobial Susceptibility Testing Panel for Imipenem, Meropenem, and Ertapenem Against Clinical Carbapenem-Resistant and Carbapenem-Susceptible Enterobacterales

Purpose: The infection of carbapenem-resistant Enterobacterales (CRE) has become a major clinical and healthcare problem worldwide. The screening methods of CRE have been extensively developed but still need improving [e.g., tests with accurate and simple minimum inhibitory (MICs)]. In this study, the performance of the BD Phoenix NMIC-413 AST panel was evaluated against clinical CRE and carbapenem-susceptible Enterobacterales (CSE) in China. The panel was first evaluated in the Chinese clinical lab.

Methods: Antimicrobial susceptibility testing of 303 clinical Enterobacterales isolates were conducted by broth microdilution (BMD), Phoenix NMIC-413 AST panel, and disk diffusion method for imipenem, ertapenem, and meropenem. Considering BMD is a gold standard, essential agreement (EA), categorical agreement (CA), minor error (MIE), major error (ME), and very major error (VME) were determined according to CLSI guidelines. CA and EA > 90%, ME <3%, and VME <1.5% were considered as acceptable criteria. Polymerase chain reaction and sanger sequencing were performed to determine the β-lactamase genotypes of CRE isolates.

Results: Three hundred and three isolates included 195 CREs and 108 CSEs were enrolled according to the BMD-MIC values of three carbapenems. Tested CREs showing 100 bla_KPC−2-positive organisms, 31 bla_IMP-positive organisms, 28 bla_NDM-positive organisms, 5 bla_VIM-positive organisms, 2 both bla_IMP and bla_VIM-positive organisms, 2 bla_OXA−48-positive organisms, and 27 isolates without carbapenemase genes. For the Phoenix NMIC-413 method, CA and EA rates >93%, MIE rates <5%, ME rates <1.75%, and VME rates were 0%, across the three drugs. For the disk diffusion method, the CA rates for three drugs were all >93%, while the MIE and ME rates were all <5 and <3%, respectively. VME rate was 3.28% for imipenem, exceeded the cut-off value specified by CLSI M52, 0 and 0.56% for ertapenem and meropenem, separately.

Conclusion: Based on the genomic data, the detection of CRE and CSE was more reliable using the BD Phoenix NMIC-413 panel compared to the BMD and disk approaches. Therefore, our study supports the use of BD Phoenix NMIC-413 panel as a suitable alternative to BMD for the detection of carbapenem resistant isolates in a clinical setting.

Bloodstream infections caused by Escherichia coli carrying mcr-1 gene in hospitalized patients in northern Italy from 2012 to 2018

PURPOSE

The recurrence of multi-drug resistant (MDR) pathogens to the latest antibiotics and the limited development of new antibacterial agents have reduced the options for the treatment of severe infections. The reintroduction of old antibiotics, such as colistin, represents an effective strategy, since the latest antibiotics are over-consumed and ineffective against MDR pathogens. In 2015, Liu (Lancet Infect Dis 16:161-168, 2016) reported Escherichia coli (E. coli) isolates carrying plasmid-mediated colistin resistance gene mcr-1. The first of mcr-1 positive colistin-resistant (col-R) E. coli from a human blood culture was observed in 2012 in Latin America, while in Italy was reported for the first time by our center in 2016. The present study aimed to describe the prevalence of mcr-1 positive col-R strains in E. coli-related bloodstream infection among patients hospitalized in Fondazione IRCCS Policlinico San Matteo in Pavia, Italy, from 2012 to 2018, including the three cases already published.

METHODS

All col-R E. coli strains isolated from blood cultures collected during the study period were analyzed. The minimal inhibitory concentration of colistin was determined using broth microdilution and detection of mcr-1 and mcr-2 genes was performed by PCR. The sequence type of E. coli mcr-1 positive was determined according to Multilocus sequence typing.

RESULTS

Out of 1557 samples, 14 strains (0.90%) were col-R. and positive for the presence of the mcr-1 gene, with no mcr-2 detected. The most common ST was ST10 (n = 3), followed by ST410 (n = 2). The remaining strains exhibited different MLST profiles, indicating that they were genetically unrelated.

CONCLUSIONS

Proper reporting of the presence of mcr-1 genes is an essential component to anticipate the spread of colistin resistance. This public health issue is particularly alarming in Italy due to the consistent circulation of MDR bacteria.