Microbial contaminants isolated from items and work surfaces in the post- operative ward at Kawolo general hospital, Uganda

Unraveling virulence determinants in extended-spectrum beta-lactamase-producing Escherichia coli from East Africa using whole-genome sequencing

Escherichia coli significantly causes nosocomial infections and rampant spread of antimicrobial resistance (AMR). There is limited data on genomic characterization of extended-spectrum β-lactamase (ESBL)-producing E. coli from African clinical settings. This hospital-based longitudinal study unraveled the genetic resistance elements in ESBL E. coli isolates from Uganda and Tanzania using whole-genome sequencing (WGS). A total of 142 ESBL multi-drug resistant E. coli bacterial isolates from both Tanzania and Uganda were sequenced and out of these, 36/57 (63.1%) and 67/85 (78.8%) originated from Uganda and Tanzania respectively. Mutations in RarD, yaaA and ybgl conferring resistances to chloramphenicol, peroxidase and quinolones were observed from Ugandan and Tanzanian isolates. We reported very high frequencies for blaCTX-M-15 with 11/18(61.1%), and blaCTX-M-27 with 12/23 (52.1%), blaTEM-1B with 13/23 (56.5%) of isolates originating from Uganda and Tanzania respectively all conferring resistance to Beta-lactam-penicillin inhibitors. We observed chloramphenicol resistance-conferring gene mdfA in 21/23 (91.3%) of Tanzanian isolates. Extraintestinal E. coli sequence type (ST) 131 accounted for 5/59 (8.4%) of Tanzanian isolates while enterotoxigenic E. coli ST656 was reported in 9/34 (26.4%) of Ugandan isolates. Virulence factors originating from Shigella dysenteriae Sd197 (gspC, gspD, gspE, gspF, gspG, gspF, gspH, gspI), Yersinia pestis CO92 (irp1, ybtU, ybtX, iucA), Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (csgF and csgG), and Pseudomonas aeruginosa PAO1 (flhA, fliG, fliM) were identified in these isolates. Overall, this study highlights a concerning prevalence and diversity of AMR-conferring elements shaping the genomic structure of multi-drug resistant E. coli in clinical settings in East Africa. It underscores the urgent need to strengthen infection-prevention controls and advocate for the routine use of WGS in national AMR surveillance and monitoring programs.Availability of WGS analysis pipeline: the rMAP source codes, installation, and implementation manual can free be accessed via https://github.com/GunzIvan28/rMAP .

Design and Application of Near Infrared LED and Solenoid Magnetic Field Instrument to Inactivate Pathogenic Bacteria

PURPOSE

This study aims to evaluate the efficiency of infrared LEDs with a magnetic solenoid field in lowering the quantity of gram-positive Staphylococcus aureus and gram-negative Escherichia coli bacteria, as well as the best exposure period and energy dose for inactivating these bacteria.

METHOD

Research has been performed on a photodynamic therapy technique called photodynamic inactivation (PDI), which combines infrared LED light with a wavelength range of 951-952 nm and a solenoid magnetic field with a strength of 0-6 mT. The two, taken together, can potentially harm the target structure biologically. Infrared LED light and an AC-generated solenoid magnetic field are both applied to bacteria to measure the reduction in viability. Three different treatments infrared LED, solenoid magnetic field, and an amalgam of infrared LED and solenoid magnetic field, were used in this study. A factorial statistical ANOVA analysis was utilized in this investigation.

RESULTS

The maximum bacterial production was produced by irradiating a surface for 60 min at a dosage of 0.593 J/cm², according to the data. The combined use of infrared LEDs and a magnetic field solenoid resulted in the highest percentage of fatalities for Staphylococcus aureus, which was 94.43 s. The highest percentage of inactivation for Escherichia coli occurred in the combination treatment of infrared LEDs and a magnetic field solenoid, namely, 72.47 ± 5.06%. In contrast, S. aureus occurred in the combined treatment of infrared LEDs and a magnetic field solenoid, 94.43 ± 6.63 percent.

CONCLUSION

Staphylococcus aureus and Escherichia coli germs are inactivated using infrared illumination and the best solenoid magnetic fields. This is evidenced by the rise in the proportion of bacteria that died in treatment group III, which used a magnetic solenoid field and infrared LEDs to deliver a dosage of 0.593 J/cm² over 60 min. According to the research findings, the magnetic field of the solenoid and the infrared LED field significantly impact the gram-positive bacteria S. aureus and the gram-negative bacteria E. coli.

The spread of antibiotic resistance to humans and potential protection strategies

Antibiotic resistance is currently one of the greatest threats to human health. Widespread use and residues of antibiotics in humans, animals, and the environment can exert selective pressure on antibiotic resistance bacteria (ARB) and antibiotic resistance gene (ARG), accelerating the flow of antibiotic resistance. As ARG spreads to the population, the burden of antibiotic resistance in humans increases, which may have potential health effects on people. Therefore, it is critical to mitigate the spread of antibiotic resistance to humans and reduce the load of antibiotic resistance in humans. This review briefly described the information of global antibiotic consumption information and national action plans (NAPs) to combat antibiotic resistance and provided a set of feasible control strategies for the transmission of ARB and ARG to humans in three areas including (a) Reducing the colonization capacity of exogenous ARB, (b) Enhancing human colonization resistance and mitigating the horizontal gene transfer (HGT) of ARG, (c) Reversing ARB antibiotic resistance. With the hope of achieving interdisciplinary one-health prevention and control of bacterial resistance.

Hospital-Based Air-Borne and Surface-Borne Bacterial Pathogens and Their Antimicrobial Profiles in Wolaita Sodo, Southern Ethiopia

Background. It is well documented that hospital environments are the niche/reservoir of many clinically important microorganisms, including multidrug-resistant air-borne and surface-borne pathogens. This problem is the most pressing public health concern, particularly in developing countries like Ethiopia, due to its poor infection management system. This study was planned to detect air-borne and surface-borne bacterial pathogens and their antimicrobial resistance patterns in Wolaita Sodo University Comprehensive Hospital, Southern Ethiopia. Method. A laboratory-based cross-sectional study was conducted from May to July 2021. Swabbing and open-plate sample collection methods were used to collect specimens. Standard bacteriological techniques were used to isolate and identify bacterial pathogens. The Mueller-Hinton agar was used to detect the drug susceptibility pattern of bacteria by using the Kirby-Bauer disc diffusion method. Result. From a total of 323 samples tested, 118 (36.5%) showed the growth of bacteria. The detection rate of bacterial pathogens in the intensive care unit (35.4%) was higher than in operation theater. From the total of 118 bacterial isolates, 39.8%, 27.9%, 20.3%, and 11.5% of S. aureus, P. aeruginosa, Klebsiella pneumoniae, and E. coli, respectively, were surface-borne. Whereas 37%, 25%, 20.83, and 16.6% of S. aureus, P. aeruginosa, Klebsiella species, and E. coli, respectively, were air-borne. S. aureus showed a 19.04 to 80.9% range of antimicrobial resistance to different classes of antibiotics from surface specimens. A 12.5–100% range of antibiotic resistance levels was detected for all Gram-negative surface-borne bacterial pathogens. P. aeruginosa was 66.7%, 73.3%, and 73.3% resistant to gentamicin, chloramphenicol, and ceftriaxone, respectively. K. pneumoniae showed 75% and 87.5% resistance to ceftriaxone and ciprofloxacin, respectively, and a completely ampicillin-resistant E. coli was detected. From a total of 48 bacterial pathogens identified from surfaces in the intensive care unit, 34 (70.8%) developed multidrug resistance. Conclusion. A significant prevalence of surface-borne bacterial pathogens was detected. This study revealed that S. aureus, P. aeruginosa, K. pneumoniae, and E. coli were nosocomial infection concerns of the hospital, and this could be the reason for different types of hospital acquired infections in the study area. A high prevalence of MDR was detected in the most surface-borne bacterial isolates.

Hospital water as the source of healthcare-associated infection and antimicrobial-resistant organisms

PURPOSE OF REVIEW

Drinking water is considered one of the most overlooked and underestimated sources of healthcare-associated infections (HAIs). Recently, the prevention and control of opportunistic premise plumbing pathogens (OPPPs) in healthcare water systems has been receiving increasing attention in infection control guidelines. However, these fail to address colonization of pathogens that do not originate from source water. Subsequently, this review explores the role of water and premise plumbing biofilm in HAIs. The potential mechanisms of contamination and transmission of antimicrobial-resistant (AMR) pathogens originating both from supply water and human microbiota are discussed.

RECENT FINDINGS

OPPPs, such as Legionella pneumophila, Pseudomonas aeruginosa and Mycobacterium avium have been described as native to the plumbing environment. However, other pathogens, not found in the source water, have been found to proliferate in biofilms formed on outlets devices and cause HAI outbreaks.

SUMMARY

Biofilms formed on outlet devices, such as tap faucets, showers and drains provide an ideal niche for the dissemination of antimicrobial resistance. Thus, comprehensive surveillance guidelines are required to understand the role that drinking water and water-related devices play in the transmission of AMR HAIs and to improve infection control guidelines.

The Importance of Monitoring the Psychological Wellbeing and Mental Health of Nursing Staff for Sustainable Management

This study examines the psychological wellbeing and mental health of nursing staff and determines workplace factors that affect them. Wellbeing and sustainable workload are important for the quality of work life. A cross-sectional study of employees in nursing was conducted at Slovenian hospitals. The response was 35%. The main findings were that more than half of employees are satisfied or very satisfied with their job and with their leaders’ support, but they are often exposed to stress. Quality of work life, work–life balance, and managing stress at the workplace affect the psychological wellbeing and mental health of nursing staff. Management should identify the importance of monitoring and improving workplace factors that can affect the employees. At the same time, they should also be aware of the importance of sustainable development of nursing employees at the local and national levels to improve the working conditions and quality of work life for better psychological wellbeing and mental health for employees.

Bacterial contamination of neglected hospital surfaces and equipment in an Algerian hospital: an important source of potential infection

Hospital surfaces are heavily contaminated with bacteria, which are a potential source of nosocomial infections. This study was undertaken to identify bacterial communities isolated from neglected hospital surfaces after cleaning routine in a Algerian public hospital. Screening of bacterial contamination in patient bed (PB), reception land-line phones (TF), door handles (DH) and medical equipment (ME) during five months generated 108 inocula. Isolates obtained were identified based on biochemical characteristics and confirmed by analysis of 16S rRNA sequences. Statistical analysis was performed to reveal possible relationship between bacterial diversity and swabbed surfaces. Our findings showed a high prevalence of bacteria in various hospital surfaces, reaching (65.25%), where a highest contaminated surface was the PB (47.22%) and a lowest contaminated was TF (5.55%). Gram negative bacteria were the dominant group (62.03%) mainly represented by Entrobacteriaceae (42.59%), whereas Staphylococcus aureus belonging to Gram positive was the main expanded pathogen with (15.74%).

Veterinary clinic surfaces as reservoirs of multi-drug- and biocide-resistant Gram-negative bacteria

This cross-sectional study was carried out to determine the common Gram-negative bacteria (GNB) contaminating veterinary clinic environments, and to evaluate the susceptibility of the isolates to commonly used antibiotics and biocides. A total of 62 swab samples were collected from different frequently touched surfaces in the 4 veterinary clinics visited. The samples were processed for isolation and identification of GNB using standard microbiological procedures. The susceptibility of the isolates to disinfectants and antibiotics was determined using agar dilution and disc diffusion techniques, respectively. A total of 114 GNB were isolated from the 4 clinics with isolation rates of 21.9, 22.8, 23.7 and 31.6% in clinics A, B, C and D, respectively. The surfaces of treatment tables were more contaminated (16.7 %) than receptionist/clinician desks (15.8%), weighing balances (10.5 %), door handles (7.9 %), drip stands (7.9 %), handwashing basins (7.0 %) and client chairs (7.0%). The surface-contaminating isolates were distributed into 20 genera, with members of Enterobacteriaceae predominating (n=97). Fifty-nine per cent of the isolates were resistant to the disinfectant Septol, while 5.3 and 0.9% were resistant to Purit and Dettol disinfectants, respectively. Multiple drug resistance was observed among 99% of the isolates with approximately 100% resistance to beta-lactams. Phenotypic expression of extended-spectrum (3.5 %) and AmpC beta-lactamase (38.6 %) production was detected. These findings highlight the role of clinic environments in serving as reservoirs for potential pathogens and sources for the spread of multi-drug resistant GNB.

Molecular Characterization of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae Isolates Collected from Inanimate Hospital Environments in Addis Ababa, Ethiopia

INTRODUCTION

The hospital environment contributes to the spread of Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE), which are contributing to increased morbidity and mortality rates. The present study was carried out to detect environmental contamination, antimicrobial susceptibility testing of ESBL-PE, and to explore molecular characterization of ESBL encoding genes.

METHODS

A cross-sectional study was conducted within the intensive care units (ICUs) of Tikur Anbessa Specialized Hospital from June to July 2018. A total of 97 swabs were taken from high-contact inanimate surfaces near immediate patient environments. All isolates were cultured by using ESBL ChromoSelect Agar and identified with conventional bacteriological methods. Antimicrobial susceptibility testing was performed as recommended by Clinical and Laboratory Standards Institute. Combination disk test was used to confirm ESBL production, while molecular characterizations of ESBL genes were performed by polymerase chain reaction.

RESULTS

Out of 97 swabbed sample, 24 (24.7%) were confirmed as ESBL-PE. The most predominant ESBL-PE was from E. coli (41.7%) and K. pneumoniae (25%). The Pediatrics and Neonatal ICU (29.2%, 7/24) exhibited highest ESBL-PE. The most contaminated materials were bed linens (33.3%). Most of ESBL-PE isolates were resistant to ampicillin (100%) and ceftriaxone (91.7%). A low resistance level was recorded for amikacin (25%). Among ESBL-producing genes, bla_CTX-M (35.7%) was the most prevalent, followed by bla_TEM and bla_SHV gene 32.1% for each.

CONCLUSIONS

Appearance of ESBL-PE in ICUs environment is posing a serious threat to control healthcare associated infections. The high level of resistance shows the need of policies for devising infection control procedures and detection of ESBL-PE.

Molecular Surveillance and Dissemination of Klebsiella pneumoniae on Frequently Encountered Surfaces in South African Public Hospitals

Bacteria that cause life-threatening illnesses in humans are also capable of contaminating hospital surfaces, thus pose as a potential source of infection. This study aimed to investigate the prevalence, genetic diversity, virulence, and antibiotic resistance profile of Klebsiella pneumoniae in South Africa. In a nonoutbreak setting involving four public hospitals, 777 samples were collected in three different wards from 11 different sites. Phenotypic and genotypic methods were used for isolation and identification. The Kirby-Bauer disk-diffusion method was used to examine antibiotic resistance followed by the combination disk method to characterize extended-spectrum β-lactamases (ESBLs). Antibiotic resistance and virulence genes were screened using PCR and clonality was investigated using enterobacterial repetitive intergenic consensus (ERIC)-PCR. Seventy-five (10%) K. pneumoniae isolates were recovered. These isolates were obtained from all four hospitals and all three wards involved. However, only six frequently touched surfaces were contaminated. Thirty (40%) isolates were characterized as ESBLs showing high resistance to antibiotics and mostly harboring the bla_CTX-M group one gene. Virulence genes were highly prevalent among all the isolates. ERIC-PCR showed that the isolates recovered from different sites within the same hospital were genetically similar. The study highlighted that K. pneumoniae can contaminate various surfaces and this persistence allows for the dissemination of bacteria within the hospital environment. The information from this study can assist hospitals to evaluate and improve current infection prevention and control interventions in place.

rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data

The recent re-emergence of multidrug-resistant pathogens has exacerbated their threat to worldwide public health. The evolution of the genomics era has led to the generation of huge volumes of sequencing data at an unprecedented rate due to the ever-reducing costs of whole-genome sequencing (WGS). We have developed the Rapid Microbial Analysis Pipeline (rMAP), a user-friendly pipeline capable of profiling the resistomes of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species) using WGS data generated from Illumina's sequencing platforms. rMAP is designed for individuals with little bioinformatics expertise, and automates the steps required for WGS analysis directly from the raw genomic sequence data, including adapter and low-quality sequence read trimming, de novo genome assembly, genome annotation, single-nucleotide polymorphism (SNP) variant calling, phylogenetic inference by maximum likelihood, antimicrobial resistance (AMR) profiling, plasmid profiling, virulence factor determination, multi-locus sequence typing (MLST), pangenome analysis and insertion sequence characterization (IS). Once the analysis is finished, rMAP generates an interactive web-like html report. rMAP installation is very simple, it can be run using very simple commands. It represents a rapid and easy way to perform comprehensive bacterial WGS analysis using a personal laptop in low-income settings where high-performance computing infrastructure is limited.

Occurrence and Phenotypic Characterization of Multidrug-Resistant Bacterial Pathogens Isolated from Patients in a Public Hospital in Mogadishu, Somalia

Purpose

This study reports a cross-sectional investigation to determine the antimicrobial resistance pattern of the common bacterial contaminants isolated from hospitalized patients in Mogadishu, Somalia.

Materials and Methods

A total of 328 clinical samples comprising urine, blood, vaginal swab, pus aspirates, and stool were collected from a public hospital located in Mogadishu the capital city of Somalia between October 2019 to March 2020. The isolation and biochemical characterization of the bacterial isolates were performed using the conventional culture and biochemical assay tests. Similarly, antimicrobial susceptibility was determined using the Kirby–Bauer disk diffusion.

Results

A total of 275 pathogenic bacteria that include Staphylococcus aureus, Escherichia coli, Pseudomonas aeroginosa, Proteus vulgare, Klebsiella pneumonia, and Salmonella spp. were detected with an overall detection rate of 78.4% (257/328). Among the bacterial pathogens isolated from clinical specimens, 152 (46.3%) were Staphylococcus aureus, 60 (18.3%) were E. coli, 10 (3.1%) Proteus vulgaris, 6 (1.8%) Klebsiella pneumonia, and 1 (0.3%) isolate was found to be Salmonella sp. The antimicrobial susceptibility assay revealed variable resistance pattern with clindamycin (40%), ampicillin (27%), vancomycin (26%), levofloxacin (23%), amoxicillin (20%), ciprofloxacin (18%) and nitrofurantoin (12%) showing the highest rate of resistance. Moreover, evaluation of multidrug resistance showed that Staphylococcus aureus had the highest multidrug resistance rate, with 19 isolates showing resistance to more than two drugs, followed by E. coli with three isolates. In contrast, each of Proteus vulgare, Salmonella sp. and Klebsiella pneumonia had one isolate each that exhibited multidrug resistance characteristics.

Conclusion

The findings of this study showed the occurrence of a number antimicrobial-resistant bacterial pathogens whose prevalence varies with age and sex. Therefore, there is a need for comprehensive antimicrobial profiling of bacterial isolates during the management of patients in the hospital.

Bacterial Profiles and Antimicrobial Susceptibility Pattern of Isolates from Inanimate Hospital Environments at Tikur Anbessa Specialized Teaching Hospital, Addis Ababa, Ethiopia

Introduction

Microbial contamination of the hospital environment plays an important role in the spread of healthcare-associated infections (HCAIs). This study was conducted to determine bacterial contamination, bacterial profiles, and antimicrobial susceptibility pattern of bacterial isolates from environmental surfaces and medical equipment.

Methods

A cross-sectional study was conducted at Tikur Anbessa Specialized Hospital (TASH) from June to September 2018. A total of 164 inanimate surfaces located at intensive care units (ICUs) and operation theaters (OTs) were swabbed. All isolates were identified by using routine bacterial culture, Gram staining, and a panel of biochemical tests. For each identified bacteria, antibiogram profiles were determined by the Kirby–Bauer disk diffusion method according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI).

Results

Out of the 164 swabbed samples, 141 (86%) were positive for bacterial growth. The predominant bacteria identified from OTs and ICUs were Staphylococci aureus (23% vs 11.5%), Acinetobacter baumannii (3.8% vs 17.5%) and coagulase-negative Staphylococcus (CoNS) (12.6% vs 2.7%) respectively. Linens were the most contaminated materials among items studied at the hospital (14.8%). Gram-positive bacteria (GPB) had significantly high resistance levels to penicillin (92.8%), cefoxitin (83.5%), and erythromycin (53.6%). On the other hand, Gram-negative bacteria (GNB) revealed the highest resistance levels to ampicillin (97.5%), ceftazidime (91.3%), ceftriaxone (91.3%), and aztreonam (90%). However, a low resistance level was recorded for amikacin (25%) followed by Ciprofloxacin (37.5%). Of the 63 S. aureus isolates, 54 (85.7%) were methicillin-resistant S. aureus (MRSA).

Conclusion

The inanimate surfaces and commonly touched medical equipment within OTs and ICUs are reservoirs of potentially pathogenic bacteria that could predispose critically ill patients to acquire HCAIs. The proportions of the antimicrobial resistance profile of the isolates are much higher from studied clean inanimate environments.

Battling Biofilm Forming Nosocomial Pathogens Using Chitosan and Pluronic F127

Biofilm represents a potential strut in bacterial treatment failure. It has a dual action; it affords microbial resistance against antibiotics and facilitate transmission of pathogenic bacteria. Nosocomial bacteria pose a serious problem in healthcare units; it prolongs patient hospital stay and increases the mortality rates beside other awful economical effect. This study was planned for targeting nosocomial bacterial biofilm using natural and biologically safe compounds like Chitosan and/or Pluronic F127. Ninety-five isolates were recovered from 107 nosocomial clinical samples. Different bacterial and fungal species were detected, from which Klebsiella pneumonia (23%), Pseudomonas aeruginosa (19%), Acinetobacter baumannii (18%) and E.coli (17%) were the predominate organisms. Pseudomonas aeruginosa, Acinetobacter baumanni and Klebsiella pneumonia were the abundant antibiotic resistant strains with multi-resistance pattern of 72%, 65% and 59%, respectively. A significant percentage of these isolates were strong biofilm forming. Herein, we investigate the effect of Chitosan and Pluronic F127 alone and in combination with each other against biofilm production. Chitosan show variable degree of biofilm inhibition, while Pluronic F127 was able to retard biofilm formation by 80% to 90% in most strain. There is no significant difference (P< 0.05) between Pluronic F127 alone and its effect in combination with Chitosan.

Water as a Source of Antimicrobial Resistance and Healthcare-Associated Infections

Healthcare-associated infections (HAIs) are one of the most common patient complications, affecting 7% of patients in developed countries each year. The rise of antimicrobial resistant (AMR) bacteria has been identified as one of the biggest global health challenges, resulting in an estimated 23,000 deaths in the US annually. Environmental reservoirs for AMR bacteria such as bed rails, light switches and doorknobs have been identified in the past and addressed with infection prevention guidelines. However, water and water-related devices are often overlooked as potential sources of HAI outbreaks. This systematic review examines the role of water and water-related devices in the transmission of AMR bacteria responsible for HAIs, discussing common waterborne devices, pathogens, and surveillance strategies. AMR strains of previously described waterborne pathogens including Pseudomonas aeruginosa, Mycobacterium spp., and Legionella spp. were commonly isolated. However, methicillin-resistant Staphylococcus aureus and carbapenem-resistant Enterobacteriaceae that are not typically associated with water were also isolated. Biofilms were identified as a hot spot for the dissemination of genes responsible for survival functions. A limitation identified was a lack of consistency between environmental screening scope, isolation methodology, and antimicrobial resistance characterization. Broad universal environmental surveillance guidelines must be developed and adopted to monitor AMR pathogens, allowing prediction of future threats before waterborne infection outbreaks occur.

How to carry out microbiological sampling of healthcare environment surfaces? A review of current evidence

There is increasing evidence that the hospital surface environment contributes to the spread of pathogens. However, evidence on how best to sample these surfaces is inconsistent and there is no guidance or legislation in place on how to do this. The aim of this review was to assess current literature on surface sampling methodologies, including the devices used, processing methods, and the environmental and biological factors that might influence results. Studies published prior to March 2019 were selected using relevant keywords from ScienceDirect, Web of Science, and PubMed. Abstracts were reviewed and all data-based studies in peer-reviewed journals in the English language were included. Microbiological air and water sampling in the hospital environment were not included. Although the numbers of cells or virions recovered from hospital surface environments were generally low, the majority of surfaces sampled were microbiologically contaminated. Of the organisms detected, multidrug-resistant organisms and clinically significant pathogens were frequently isolated and could, therefore, present a risk to vulnerable patients. Great variation was found between methods and the available data were incomplete and incomparable. Available literature on sampling methods demonstrated deficits with potential improvements for future research. Many of the studies included in the review were laboratory-based and not undertaken in the real hospital environment where sampling recoveries could be affected by the many variables present in a clinical environment. It was therefore difficult to draw overall conclusions; however, some recommendations for the design of routine protocols for surface sampling of healthcare environments can be made.

Investigating colistin drug resistance: The role of high-throughput sequencing and bioinformatics

Bacterial infections involving antibiotic-resistant gram-negative bacteria continue to increase and represent a major global public health concern. Resistance to antibiotics in these bacteria is mediated by chromosomal and/or acquired resistance mechanisms, these give rise to multi-drug resistant (MDR), extensive-drug resistant (XDR) or pan-drug resistant (PDR) bacterial strains. Most recently, plasmid-mediated resistance to colistin, an antibiotic that had been set apart as the last resort antibiotic in the treatment of infections involving MDR, XDR and PDR gram-negative bacteria has been reported. Plasmid-mediated colistin resistant gram-negative bacteria have been described to be PDR, implying a state devoid of alternative antibiotic therapeutic options. This review concisely describes the evolution of antibiotic resistance to plasmid-mediated colistin resistance and discusses the potential role of high-throughput sequencing technologies, genomics, and bioinformatics towards improving antibiotic resistance surveillance, the search for novel drug targets and precision antibiotic therapy focused at combating colistin resistance, and antibiotic resistance as a whole.

Investigating colistin drug resistance: The role of high-throughput sequencing and bioinformatics

Bacterial infections involving antibiotic resistant gram-negative bacteria continue to increase and represent a major global public health concern. Resistance to antibiotics in these bacteria is mediated by chromosomal and/or acquired resistance mechanisms, these give rise to multi-drug resistant (MDR) or extensive drug resistant (XDR) bacterial strains. Most recently, a novel acquired plasmid mediated resistance mechanism to colistin, an antibiotic that had been set apart as the last resort antibiotic in the treatment of infections involving MDR and XDR gram-negative bacteria, has been reported. Plasmid mediated colistin resistant gram-negative bacteria have been described to be pan-drug resistant, implying a state devoid of alternative antibiotic therapeutic options. This review describes the evolution of antibiotic resistance to plasmid mediated colistin resistance, and discusses the potential role of high-throughput sequencing technologies, genomics and bioinformatics towards improving antibiotic resistance surveillance, the search for novel drug targets and precision antibiotic therapy focused at combating colistin resistance, and antimicrobial resistance as a whole.