Functional Genome Screening to Elucidate the Colistin Resistance Mechanism

Molecular prevalence of resistance determinants, virulence factors and capsular serotypes among colistin resistance carbapenemase producing Klebsiella pneumoniae: a multi-centric retrospective study

The emergence of colistin-carbapenem-resistant Klebsiella pneumoniae (CCR-Kp) in bloodstream infection results in high mortality, and virulence factor contributes further to the difficulty of treatment. A total of 158 carbapenem-resistant K. pneumoniae (CRKP) isolates causing bloodstream infection were collected from three Indian tertiary care hospitals during the 9-month study period, of which 27 isolates exhibited resistance to both colistin and carbapenem antibiotics. In this study, all the strains were characterized for antimicrobial resistance, virulence factors and capsular serotypes that facilitate the development of colistin and carbapenem-resistant K.pneumoniae (CCR-Kp) in bloodstream infection. Fourteen isolates displayed extremely drug resistance (XDR), susceptible only to tigecycline, and the remaining 13 isolates displayed multidrug resistance (MDR). The gene prevalence analysis for CCR-Kp isolates showed the predominance of bla KPC (81.48%) followed by bla NDM (62.96%), bla VIM (37.03%) and bla IMP (18.51%) genes. The distribution of virulence genes was found to be fimH (81.48%), wabG (59.25%), mrkD (55.56%), entB (48.15%), irp1 (33.33%), and rmpA (18.52%). The capsular serotypes K1, K2, K5 and K54 have been identified in 16 isolates. The absence of plasmid-mediated colistin resistance (mcr) genes implies the involvement of other mechanisms. The ERIC and (GTG)5 molecular typing methods detected 18 and 22 distinct clustering patterns among the CCR-Kp isolates, respectively. A strong correlation between ERIC and (GTG)5 genotyping method was established with antimicrobial resistance patterns and virulence determinants at P < 0.05, while no correlation was found with capsular serotyping. Similar virulence and resistance typing among the isolates suggest hospital-acquired infection in a health care setup. These outcomes will advance our awareness of CCR-Kp outbreaks associated with tertiary care hospitals and help forecast their occurrence in the near future.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03056-4.

Colistin resistance in Gram-negative bacteria analysed by five phenotypic assays and inference of the underlying genomic mechanisms

BACKGROUND

Colistin is used against multi-drug resistant pathogens, yet resistance emerges through dissemination of plasmid-mediated genes (mcr) or chromosomal mutation of genes involved in lipopolysaccharide synthesis (i.e. mgrB, phoPQ, pmrCAB). Phenotypic susceptibility testing is challenging due to poor diffusion of colistin in agar media, leading to an underestimation of resistance. Performance of five phenotypic approaches was compared in the context of different molecular mechanisms of resistance. We evaluated Vitek 2® (bioMérieux, AST N242), Colistin MIC Test Strip (Liofilchem Diagnostici), UMIC (Biocentric), and Rapid Polymyxin™ NP test (ELITechGroup) against the standard broth microdilution (BMD) method. We used whole genome sequencing (WGS) to infer molecular resistance mechanisms. We analysed 97 Enterobacterales and non-fermenting bacterial isolates, largely clinical isolates collected up to 2018. Data was analysed by comparing susceptibility categories (susceptible or resistant) and minimal inhibitory concentrations (MIC). Susceptibility category concordance is the percentage of test results sharing the same category to BMD. MIC concordance was calculated similarly but considering ±1 MIC titre error range. We determined genomic diversity by core genome multi locus sequencing typing (cgMLST) and identified putative antimicrobial resistance genes using NCBI and CARD databases, and manual annotation.

RESULTS

Of 97 isolates, 54 (56%) were resistant with standard BMD. Highest susceptibility category concordance was achieved by Rapid Polymyxin™ NP (98.8%) followed by UMIC (97.9%), Colistin E-test MIC strip (96.9%) and Vitek 2® (95.6%). Highest MIC concordance was achieved by UMIC (80.4%), followed by Vitek 2® (72.5%) and Colistin E-test MIC strip (62.9%). Among resistant isolates, 23/54 (43%) were intrinsically resistant to colistin, whereas 31/54 (57%) isolates had acquired colistin resistance. Of these, mcr-1 was detected in four isolates and mcr-2 in one isolate. Non-synonymous mutations in mgrB, phoQ, pmrA, pmrB, and pmrC genes were encountered in Klebsiella pneumoniae, Escherichia coli, and Acinetobacter bereziniae resistant isolates. Mutations found in mgrB and pmrB were only identified in isolates exhibiting MICs of ≥16 mg/L.

CONCLUSIONS

The Rapid Polymyxin™ NP test showed highest categorical concordance and the UMIC test provided MIC values with high concordance to BMD. We found colistin resistance in diverse species occurred predominantly through spontaneous chromosomal mutation rather than plasmid-mediated resistance.

Regulation of Virulence by Two-Component Systems in Pathogenic Burkholderia

The regulation and timely expression of bacterial genes during infection is critical for a pathogen to cause an infection. Bacteria have multiple mechanisms to regulate gene expression in response to their environment, one of which is two-component systems (TCS). TCS have two components. One component is a sensory histidine kinase (HK) that autophosphorylates when activated by a signal. The activated sensory histidine kinase then transfers the phosphoryl group to the second component, the response regulator, which activates transcription of target genes. The genus Burkholderia contains members that cause human disease and are often extensively resistant to many antibiotics. The Burkholderia cepacia complex (BCC) can cause severe lung infections in patients with cystic fibrosis (CF) or chronic granulomatous disease (CGD). BCC members have also recently been associated with several outbreaks of bacteremia from contaminated pharmaceutical products. Separate from the BCC is Burkholderia pseudomallei, which is the causative agent of melioidosis, a serious disease that occurs in the tropics, and a potential bioterrorism weapon. Bioinformatic analysis of sequenced Burkholderia isolates predicts that most strains have at least 40 TCS. The vast majority of these TCS are uncharacterized both in terms of the signals that activate them and the genes that are regulated by them. This review will highlight TCS that have been described to play a role in virulence in either the BCC or B. pseudomallei Since many of these TCS are involved in virulence, TCS are potential novel therapeutic targets, and elucidating their function is critical for understanding Burkholderia pathogenesis.

A severe leakage of intermediates to shunt products in acarbose biosynthesis

The α-glucosidase inhibitor acarbose, produced by Actinoplanes sp. SE50/110, is a well-known drug for the treatment of type 2 diabetes mellitus. However, the largely unexplored biosynthetic mechanism of this compound has impeded further titer improvement. Herein, we uncover that 1-epi-valienol and valienol, accumulated in the fermentation broth at a strikingly high molar ratio to acarbose, are shunt products that are not directly involved in acarbose biosynthesis. Additionally, we find that inefficient biosynthesis of the amino-deoxyhexose moiety plays a role in the formation of these shunt products. Therefore, strategies to minimize the flux to the shunt products and to maximize the supply of the amino-deoxyhexose moiety are implemented, which increase the acarbose titer by 1.2-fold to 7.4 g L⁻¹. This work provides insights into the biosynthesis of the C₇-cyclitol moiety and highlights the importance of assessing shunt product accumulation when seeking to improve the titer of microbial pharmaceutical products.

Biosynthetic mechanism for the type 2 diabetes treatment drug acarbose is not fully revealed. Here, the authors show that shunt pathways and inefficient amino-deoxyhexose biosynthesis lead to 1-epi-valienol and valienol accumulation, and minimizing the flux to these shunt products can increase acarbose titer in Actinoplanes species.

Genotypic validation of extended-spectrum β-lactamase and virulence factors in multidrug resistance Klebsiella pneumoniae in an Indian hospital

The emergence of extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae has been increasing rapidly across the world. The presence of virulence factors in ESBL producers further adds to the pathogenicity and severity of infection, which often complicate empirical therapy and sometimes result in treatment failures. In the present study, 227 non-repeated clinical isolates of K. pneumoniae obtained from different clinical specimens from a tertiary care hospital in India were analyzed to detect the genes responsible for ESBL production (blaTEM, blaCTX-M, and blaSHV), virulence (fimH-1, mrkD, entB, irp-1), and capsule production (K1-K2). Phenotypically identified 72 ESBL producing K. pneumoniae isolates were further subjected to PCR based genotypic analysis but only 20 were found to have at least one of the ESBL producing genes. blaTEM was the most predominant gene (100%), followed by blaSHV (90%), and blaCTX-M (85%). Similarly, the most common virulence genes were fimH-1 (70%), entB (65%), markD (55%), irp-1 (25%), K1 (25%), and K2 (20%). REP-PCR profile separated them into five major clusters (I-V), indicating the existing heterogeneity among the isolates. The resistance profile data obtained from the present study can serve as the information base to understand the infection pattern prevailing in the hospital and for physicians to recommend suitable antibiotics for the patients.

How to discover new antibiotic resistance genes?

INTRODUCTION

Antibiotic resistance (AR) is a worldwide concern and the description of AR have been discovered mainly because of their implications in human medicine. Since the recent burden of whole-genome sequencing of microorganisms, the number of new AR genes (ARGs) have dramatically increased over the last decade. Areas covered: In this review, we will describe the different methods that could be used to characterize new ARGs using classic or innovative methods. First, we will focus on the biochemical methods, then we will develop on molecular methods, next-generation sequencing and bioinformatics approaches. The use of various methods, including cloning, mutagenesis, transposon mutagenesis, functional genomics, whole genome sequencing, metagenomic and functional metagenomics will be reviewed here, outlining the advantages and drawbacks of each method. Bioinformatics softwares used for resistome analysis and protein modeling will be also described. Expert opinion: Biological experiments and bioinformatics analysis are complementary. Nowadays, the ARGs described only account for the tip of the iceberg of all existing resistance mechanisms. The multiplication of the ecosystems studied allows us to find a large reservoir of AR mechanisms. Furthermore, the adaptation ability of bacteria facing new antibiotics promises a constant discovery of new AR mechanisms.

Molecular mechanisms of polymyxin resistance: knowns and unknowns

Colistin, also referred to as polymyxin E, is an effective antibiotic against most multidrug-resistant Gram-negative bacteria and is currently used as a last-line drug for treating severe bacterial infections. Colistin resistance has increased gradually for the last few years, and knowledge of its multifaceted mechanisms is expanding. This includes the newly discovered plasmid-mediated colistin resistance gene mcr-1, which has been detected in over 20 countries within 3 months of its first report. We previously reported all of the known mechanisms of polymyxin resistance in our first review in 2014, but an update seems necessary in 2016, considering the significant recent discoveries that have been made in this domain. This review provides an update about what is already known, what is new, and some unresolved questions with respect to colistin resistance.