SummaryA literature review was undertaken to ascertain the molecular basis for tigecycline and colistin resistance mechanisms and the experimental basis for the detection and delineation of this resistance particularly in carbapenemaseproducing Gram-negative bacteria. Pubmed, Google Scholar and Science Direct were searched with the keywords colistin, tigecycline, resistance mechanisms and detection methods. Trans-complementation and comparative MIC studies, mass spectrometry, chromatography, spectrofluorometry, PCR, qRT-PCR and whole genome sequencing (WGS) were commonly used to determine tigecycline and colistin resistance mechanisms, specifically modifications in the structural and regulatory efflux (acrAB, OqxAB, kpgABC adeABC-FGH-IJK, mexAB-XY-oprJM and soxS, rarA robA, ramRAB marRABC, adeLRS, mexRZ and nfxb) and lipid A (pmrHFIJFKLM, lpxA, lpxC lpxD and mgrB, pmrAB, phoPQ,) genes respectively. Mutations in the ribosomal 16S rRNA operon rrnBC, also yielded resistance to tigecycline through target site modifications. The mcr-1 gene conferring resistance to colistin was identified via WGS, transcomplementation and a murine thigh infection model studies. Common detection methods are mainly antibiotic sensitivity testing with broth microdilution while molecular identification tools are mostly PCR and WGS. Spectrofluorometry, MALDI-TOF MS, micro-array and real-time multiplex PCR hold much promise for the future as new detection tools.

Whole-genome sequence analyses revealed the presence of ( = 31), ( = 8), ( = 1), or ( = 1) in extensively drug-resistant and pandrug-resistant organisms isolated from in-patients in 10 private hospitals (2012 to 2013) in Durban, South Africa. Two novel NDM-1-encoding plasmids from were circularized by PacBio sequencing. In p19-10_01 [IncFIB(K); 223.434 bp], was part of a Tn-like structure (16.276 bp) delineated by IS The multireplicon plasmid p18-43_01 [IncR_1/IncFIB(pB171)/IncFII(Yp); 212.326 bp] shared an 80-kb region with p19-10_01, not including the -containing region. The two plasmids were used as references for tracing NDM-1-encoding plasmids in the other genome assemblies. The p19-10_01 sequence was detected in ( = 7) only, whereas p18-43_01 was tracked to ( = 4), ( = 1), ( = 11), spp. ( = 7), and ( = 1), revealing horizontal spread of this -bearing plasmid structure. Global phylogeny showed clustering of the (18/20) isolates together with closely related carbapenemase-negative ST101 isolates from other geographical origins. The South African isolates were divided into three phylogenetic subbranches, where each group had distinct resistance and replicon profiles, carrying either p19-10_01, p18-10_01, or pCHE-A1 (8,201 bp). The latter plasmid carried and within an integron mobilization unit. Our findings imply independent plasmid acquisition followed by local dissemination. Additionally, we detected carried by pPKPN4 in (ST14) and contained by a pNDM-MGR194-like genetic structure in (ST167), adding even more complexity to the multilayer molecular mechanisms behind nosocomial spread of carbapenem-resistant in Durban, South Africa.

BackgroundMultidrug-resistant Gram-negative bacteria have emerged as major clinical and therapeutic dilemma in hospitals in Ghana.To describe the prevalence and profile of infections attributable to multidrug-resistant Gram-negative bacteria among patients at the Komfo Anokye Teaching Hospital in the Ashanti region of Ghana.MethodsBacterial cultures were randomly selected from the microbiology laboratory from February to August, 2015. Bacterial identification and minimum inhibitory concentrations were conducted using standard microbiological techniques and the Vitek-2 automated system. Patient information was retrieved from the hospital data.ResultsOf the 200 isolates, consisting of K. pneumoniae, A. baumannii, P. aeruginosa, Enterobacter spp., E. coli, Yersinia spp., Proteus mirabilis, Pasteurella spp., Chromobacterium violaceum, Salmomella enterica, Vibrio spp., Citrobacter koseri, Pantoea spp., Serratia spp., Providencia rettgeri Burkholderia cepacia, Aeromonas spp., Cadecea lapagei and Sphingomonas paucimobilis, 101 (50.5%) and 99 (49.5%) recovered from male and female patients respectively The largest proportion of patients were from age-group ≥60 years (24.5%) followed by < 10 years (24.0%) and least 10–19 years (9.5%) with a mean patient age of 35.95 ± 27.11 (0.2–91) years. The decreasing order of specimen source was urine 97 (48.5%), wound swabs 47 (23.5%), sputum 22 (11.0%) bronchial lavage, nasal and pleural swabs 1 (0.50%). Urinary tract infection was diagnosed in 34.5% of patients, sepsis in 14.5%, wound infections (surgical and chronic wounds) in 11.0%, pulmonary tuberculosis in 9.0% and appendicitis, bacteremia and cystitis in 0.50%. The isolates showed high resistance to ampicillin (94.4%), trimethoprim/sulfamethoxazole (84.5%), cefuroxime (79.0%) and cefotaxime (71.3%) but low resistance to ertapenem (1.5%), meropenem (3%) and amikacin (11%). The average multi-drug resistance was 89.5%, and ranged from 53.8% in Enterobacter spp. to 100.0% in Acinetobacter spp. and P. aeruginosa.ConclusionBacterial infections caused by multi-drug resistant (isolates resistant to at least one agent in three or more antibiotic classes) Gram-negative pathogens among patients at Komfo Anokye Teaching Hospital in Kumasi, Ghana are rife and interventions are necessary for their containment.

Research articles describing carbapenemases and their genetic environments in Gram-negative bacteria were reviewed to determine the molecular epidemiology of carbapenemases in Africa. The emergence of resistance to the carbapenems, the last resort antibiotic for difficult to treat bacterial infections, affords clinicians few therapeutic options, with a resulting increase in morbidities, mortalities, and healthcare costs. However, the molecular epidemiology of carbapenemases throughout Africa is less described. Research articles and conference proceedings describing the genetic environment and molecular epidemiology of carbapenemases in Africa were retrieved from Google Scholar, Scifinder, Pubmed, Web of Science, and Science Direct databases. Predominant carbapenemase genes so far described in Africa include the blaOXA-48 type, blaIMP, blaVIM, and blaNDM in Acinetobacter baumannii, Klebsiella pneumoniae, Enterobacter cloacae, Citrobacter spp., and Escherichia coli carried on various plasmid types and sizes, transposons, and integrons. Class D and class B carbapenemases, mainly prevalent in A. baumannii, K. pneumoniae, E. cloacae, Citrobacter spp., and E. coli were the commonest carbapenemases. Carbapenemases are mainly reported in North and South Africa as under-resourced laboratories, lack of awareness and funding preclude the detection and reporting of carbapenemase-mediated resistance. Consequently, the true molecular epidemiology of carbapenemases and their genetic environment in Africa is still unknown.

SummaryThe minimal antibiotic options for carbapenemase-producing Gram-negative bacteria necessitate their rapid detection. A literature review of a variety of phenotypic and genotypic methods is presented. Advances in culture methods and screening media are still subject to long incubation hours. Biochemical methods have shorter turnaround times and higher sensitivities and specificities, but cannot differentiate between various types and variants. Spectrophotometric methods are cheap and efficient, but are uncommon in many clinical settings, while the MALDI-TOF MS is promising for species identification, typing and resistance gene determination. Although next generation sequencing (NGS) technologies provide a better platform to detect, type and characterize carbapenem-resistant bacteria, the different NGS platforms, the large computer memories and space needed to process and store genomic data and the nonuniformity in data analysis platforms are still a challenge. The sensitivities, specificities and turnaround times recorded in the various studies reviewed favours the use of the biochemical tests (Carba NP or Rapid Carb screen tests) for the detection of putative carbapenemaseproducing isolates. MALDI-TOF MS and/or molecular methods like microarray, loop-mediated isothermal amplification and real-time multiplex PCR assays could be used for further characterization in a reference laboratory. NGS may be used for advanced epidemiological and molecular studies.