Molecular Characteristics and Antibiotic Resistance Profiles of Klebsiella Isolates in Mthatha, Eastern Cape Province, South Africa

Epidemiology of Community-acquired Bacteremia Among Children One to Fifty-nine Months of Age Admitted to a Tertiary Hospital in Harar, Eastern Ethiopia

BACKGROUND

Community-acquired bacteremia is a leading cause of mortality in children <5 years of age in Ethiopia, yet data on etiology are scarce. We described the etiology and risk factors for bacteremia and in-hospital mortality in a tertiary hospital in eastern Ethiopia.

METHODS

Clinical surveillance was conducted at Hiwot Fana Comprehensive Specialized Hospital from December 2021 to November 2023. All admitted children 29 days to 59 months old were eligible for blood culture collection, excluding elective surgery or poisoning.

RESULTS

Of 3384 admissions, 2366 were sampled; 2070 had uncontaminated blood cultures, and 236 (11.4%) had bacteremia. The incidence risk was 69.7 per 1000 admissions. Klebsiella oxytoca (n = 59, 25.0%) and Klebsiella pneumoniae (n = 30, 12.7%) were the most common pathogens. The leading gram-positive pathogen was Streptococcus pneumoniae (n = 16, 6.8%). Gram-negative bacteria showed high resistance to ampicillin and gentamicin. Out of 2070, 122 died, yielding a case fatality ratio of 13.1% in bacteremia cases compared to 5.0% in nonbacteremic cases. Severe wasting [adjusted odds ratio, 1.49, (95% confidence interval: 1.10-2.01)] was associated with bacteremia risk. Bacteremic cases had a high risk of death across all nutritional statuses, while nonbacteremic admissions exhibited increased mortality risk with the severity of the nutritional status.

CONCLUSION

A high proportion of children admitted to Hiwot Fana Comprehensive Specialized Hospital had bacteremia with attendant high mortality. K. oxytoca was the commonest cause, showing significant resistance to first-line antimicrobials.

Genomic analysis of virulent, multidrug resistant Klebsiella pneumoniae and Klebsiella oxytoca from bloodstream infections, South Africa

The study investigated the resistome, virulome and mobilome of multidrug resistant (MDR) Klebsiella pneumoniae and Klebsiella oxytoca clinical isolates.

METHODS

A total of 46 suspected Klebsiella species (spp.) were collected from blood cultures within the uMgungundlovu District in the KwaZulu-Natal Province. Antibiotic susceptibility was determined against a panel of 19 antibiotics using the disk diffusion test. A subset of 14 MDR K. pneumoniae (n = 10) and K. oxytoca (n = 4) isolates were selected based on their antibiograms and subjected to whole genome sequencing (WGS). The sequence types (STs), resistome, virulome, mobilome, capsule loci (KLs) were analysed using relevant WGS and bioinformatics tools.

RESULTS

Of the 10 K. pneumoniae sequence types (ST) identified, the most common were ST25 (n = 3), ST101 (n = 3), and 4 K. oxytoca belonged to ST450 (n = 3). The two high-risk K. pneumoniae clones ST15, and ST17 were identified. O and K capsule types were identified, with predominance of KL2, KL17, KL29, O1/O2v2, O1/O2v1, and OL104 respectively. The majority of isolates displayed multidrug resistance predominantly carrying β-lactamase genes, including blaCTX-M-15, blaTEM-1B, blaSHV, and blaOXA-1, and blaOXY including the carbapenemase blaOXA-181 in two (14.3 %) study isolates. Other resistance genes included: aac(6')-lb-cr, aac(3), aac, aph, aad, dfr, tet(A), and tet(D), mph(A), sul1, sul2, oqx, qnr, acrR, ramR, parC, gyrA, arr-3, cat, fosA, qacE genes conferring resistance to aminoglycosides, trimethoprim, tetracycline, macrolide, sulfonamides, fluoroquinolones, rifampicin phenicols, fosfomycin, and quaternary ammonium compound disinfectant. Virulence factors related to hypervirulence: encoding aerobactin (iuc, iutA), salmochelin (iro), yersiniabactin (ybt), enterobactin (ent), type 1 and 3 (mrk and fim), and capsule synthesis (rcsA and rcsB) were identified. IncF, IncR, and Col plasmid replicon types and class I integrons were detected, with IncFIB(K) predominance. The blaCTX-M-15 and blaTEM-1 genes were bracketed by Tn3 transposons, ISEc9, recombinase and IS91 insertion sequences.

CONCLUSIONS

The convergence of multidrug resistance and hypervirulence genes in Klebsiella strains is a potential clinical concern. Carbapenemase, ESBL screening and genomic surveillance are urgently required in hospital environments.

Antibiotic resistance and biofilm formation in Klebsiella spp. isolates from Intensive Care Units in the Brazilian Amazon

Klebsiella spp. is an opportunistic pathogen which poses a significant threat to public health, especially due to antimicrobial resistance and biofilm formation. This study aimed to determine the antibiotic resistance profile, biofilm formation and β-lactamases production in Klebsiella spp. strains from clinical samples obtained from hospitalized patients, health professionals and hospital environment of intensive care units (ICUs) in Brazilian Amazon. The strains were obtained from clinical samples in different hospitals and identified using molecular techniques. The antimicrobial susceptibility was investigated via disk diffusion and microdilution. Biofilm formation was evaluated using a microtiter plate assay, while the extended-spectrum β-lactamases (ESBL) and carbapenemases production was assessed via disk approximation tests and combined disk tests, respectively. A total of 226 Klebsiella spp. strains were identified, with 141 coming from patients hospitalized in ICUs, 54 from healthcare workers, and 31 from hospital structures. Collection sites that showed the highest frequencies of isolated bacteria were the armpit (43,3%), oral cavity (42.6%), nasal cavity (70.4%), beds (54.8%) and mechanical ventilation (19.4%). Klebsiella spp. isolates from hospitalized patients and hospital ICU environments showed a high frequency of resistance (>50%) to the antibiotics, cefuroxime, cefotaxime, ceftriaxone, ciprofloxacin and aztreonam, and greater sensitivity (>70%) to carbapenems, amikacin and polymyxin B. Samples obtained from hospital structures (74.2%) and patients (51.8%) exhibited a high rate of multidrug resistant (MDR) isolates. In addition, 29% of Klebsiella isolates were found to produce ESBL and 15.5% carbapenemases. Biofilm formation was observed in 58.4% (132/226) of the isolates, with percentages of 64.5% (91/141) in hospitalized patients, 51.6% (16/31) on hospital structures, and 46.3% (25/54) among healthcare professionals. These results indicated a high percentage of antibiotics resistance and MDR in isolates from hospital structures and patients, which also showed ability to produce biofilms, ESBL and carbapenemases. Our findings reinforce the need to monitor resistance and adopt measures aimed at preventing the spread of MDR bacteria in ICUs.

Prevalence and antimicrobial resistance of Enterobacteriaceae in the north of Kazakhstan

Background

An increasing number of drugs are used each year in the treatment of small pets (cats and dogs), including medicines (cephalosporins and fluoroquinolones) used in human therapy.

Aim

The purpose of this study was to isolate and explore the antibiotic resistance of opportunistic Enterobacteriaceae (Escherichia coli, Klebsiella, Proteus, Ci trobacter, Enterobacter) from cats and dogs, and to isolate resistance genes in the microorganisms.

Methods

In 2021, 808 samples of biological material from small domestic animals were collected in veterinary clinics in Kostanay. From these, 210 microorganisms were isolated and identified.

Results

A large majority of the strains sampled belonged to E. coli-149 (70.9%), Enterobacter-11 (5.2%), Klebsiella-28 (13.3%), Proteus-12 (5.7%) and 10 Citrobacter isolates (4.8%). In all isolates identified, antibiotic resistance/sensitivity was determined by disc-diffusion method to ampicillin, cefoxitin, gentamicin, levomycetin, tetracycline, ciprofloxacin, norfloxacin, ofloxacin, cefoperazone, cefpodoxime, streptomycin, kanamycin, doxycycline, gemifloxacin, nalidixic acid, furazolidone, furadonine, amoxicillin, and enrofloxacin.

Conclusion

The study has demonstrated that the greatest number of Enterobacteriaceae were sensitive to the action of meropenem, which belongs to the group of beta-lactam antibiotics; resistance was demonstrated against tetracycline, doxycycline, ampicillin, amoxicillin, ofloxacin, and cefpodoxime. The most common genes encoding antimicrobial resistance were as follows: BlaTEM and OXA in 41 and 28 isolates, respectively, encoding resistance to beta-lactams; StrA and StrB in 45 and 48 isolates encoding aminoglycosides; and tetA and tetB in 43 and 28 isolates encoding tetracyclines. Obtained data demonstrate that uncontrolled and frequent use of beta-lactam and tetracycline antibacterials, in cats and dogs, results in the spread of genotypic resistance among micro-organisms of the family Enterobacteriaceae.

Genotypic Determination of Extended Spectrum β-Lactamases and Carbapenemase Production in Clinical Isolates of Klebsiella pneumoniae in Southwest Nigeria

INTRODUCTION

Klebsiella pneumoniae is a major pathogen implicated in healthcare-associated infections. Extended-spectrum β-lactamase (ESBL) and carbapenemase-producing K. pneumoniae isolates are a public health concern. This study investigated the existence of some ESBL and carbapenemase genes among clinical isolates of K. pneumoniae in Southwest Nigeria and additionally determined their circulating clones.

MATERIALS AND METHODS

Various clinical samples from 420 patients from seven tertiary hospitals within Southwestern Nigeria were processed between February 2018 and July 2019. These samples were cultured on blood agar and MacConkey agar, and the isolated bacteria were identified by Microbact GNB 12E. All K. pneumoniae were confirmed by polymerase chain reaction (PCR) using the 16s rRNA gene. Antibiotic susceptibility testing (AST) was done on these isolates, and the PCR was used to evaluate the common ESBL-encoding genes and carbapenem resistance genes. Genotyping was performed using multi-locus sequencing typing (MLST).

RESULTS

The overall prevalence of K. pneumoniae in Southwestern Nigeria was 30.5%. The AST revealed high resistance rates to tetracyclines (67.2%), oxacillin (61.7%), ampicillin (60.2%), ciprofloxacin (58.6%), chloramphenicol (56.3%), and lowest resistance to meropenem (43.0%). All isolates were susceptible to polymyxin B. The most prevalent ESBL gene was the TEM gene (47.7%), followed by CTX-M (43.8%), SHV (39.8%), OXA (27.3%), CTX-M-15 (19.5%), CTX-M-2 (11.1%), and CTX-M-9 (10.9%). Among the carbapenemase genes studied, the VIM gene (43.0%) was most detected, followed by OXA-48 (28.9%), IMP (22.7%), NDM (17.2%), KPC (13.3%), CMY (11.7%), and FOX (9.4%). GIM and SPM genes were not detected. MLST identified six different sequence types (STs) in this study. The most dominant ST was ST307 (50%, 5/10), while ST258, ST11, ST147, ST15, and ST321 had (10%, 1/10) each.

CONCLUSION

High antimicrobial resistance in K. pneumoniae is a clear and present danger for managing infections in Nigeria. Additionally, the dominance of a successful international ST307 clone highlights the importance of ensuring that genomic surveillance remains a priority in the hospital environment in Nigeria.

Detection of CTX-M and SHV Genes in Extended Spectrum Beta-Lactamase Producing Klebsiella Pneumoniae and Pseudomonas Aeruginosa in a Tertiary Hospital in North-central Nigeria

Background

Antimicrobial resistance (AMR) is an emerging threat to global health security. Globally, an estimated 700,000 deaths are attributed to AMR annually. Annual deaths due to AMR are projected to reach 10 million by 2050 if current trends persist. Extended Spectrum β-Lactamases (ESBLs) have the ability to hydrolyse penicillins, cephalosporins up to the third generation, and monobactams, but not β-lactamase inhibitors such as clavulanic acid. ESBLs undergo continuous mutation, leading to the development of new enzymes with over 400 different ESBL variants described. This study aimed to detect selected CTX-M genes, SHV,and TEM genes in Extended Spectrum Beta-Lactamase producing Klebsiella pneumoniae and Pseudomonas aeruginosa in Jos, Nigeria.

Methodology

A total of 110, non-replicated isolates of Klebsiella pneumonia and 125 isolates of Pseudomonas aeruginosa were identified phenotypically from clinical specimens of patients at a tertiary hospital in Jos, North-central Nigeria. The isolates were screened for ESBL production using the disk diffusion method of the Clinical Laboratory Standard Institute (CLSI) breakpoints. Phenotypic confirmation of ESBL production was done using the double-disc synergy test. Multiplex PCR was used to detect ESBL genes.

Results

Fifty (45.5%) of the 110 isolates of Klebsiella pneumoniae and 9(7.2%) of the 125 isolates of Pseudomonas aeruginosa were ESBL-positive. Typing of 20 representative ESBL isolates (17 Klebsiella and 3 Pseudomonas spp) showed the presence ofblaCTX-M1, blaCTX-M9, and blaSHV genes in these isolates. All 20 (100%) isolates had the blaCTX-M1 gene. The blaSHV gene was detected in 16(80%) while CTX-M9 was detected in 6(30%) of the isolates studied.

Conclusion

The study showed that there is a high prevalence of ESBL genes among isolates ofKlebsiella pneumoniae and Pseudomonas aeruginosa in North-central Nigeria. This emphasizes the need for continuous surveillance and coordinated infection prevention and control to curtail its spread.

Antibiotic resistance and the alternatives to conventional antibiotics: The role of probiotics and microbiota in combating antimicrobial resistance

From the introduction of the first antibiotic to the present day, the emergence of antibiotic resistance has been a difficult problem for medicine. Regardless of the type of antibiotic resistance, the presence of resistant isolates in clinical and even asymptomatic fecal carriers becomes a difficult public health problem. Therefore, the use of new antimicrobial combination therapies or alternative agents with antimicrobial activity that have the least side effects, including plant-, metal-, and nanoparticle-based agents, could be crucial and useful. Recently, the use of probiotics as a hypothetical candidate to combat infectious disease control and antimicrobial resistance has received notable attention. Considering the alteration of the microbiota in fecal carriers and also in patients with resistant bacterial isolates, the use of probiotics could have an appropriate effect on the balance of the microbial population. In this review, we have attempted to discuss the history of antimicrobial resistance and provide an overview of microbiota change and the use of probiotics as new agents with antimicrobial activity associated with the emergence of resistant isolates.

ESKAPE Pathogens: Looking at Clp ATPases as Potential Drug Targets

Bacterial antibiotic resistance is rapidly growing globally and poses a severe health threat as the number of multidrug resistant (MDR) and extensively drug-resistant (XDR) bacteria increases. The observed resistance is partially due to natural evolution and to a large extent is attributed to antibiotic misuse and overuse. As the rate of antibiotic resistance increases, it is crucial to develop new drugs to address the emergence of MDR and XDR pathogens. A variety of strategies are employed to address issues pertaining to bacterial antibiotic resistance and these strategies include: (1) the anti-virulence approach, which ultimately targets virulence factors instead of killing the bacterium, (2) employing antimicrobial peptides that target key proteins for bacterial survival and, (3) phage therapy, which uses bacteriophages to treat infectious diseases. In this review, we take a renewed look at a group of ESKAPE pathogens which are known to cause nosocomial infections and are able to escape the bactericidal actions of antibiotics by reducing the efficacy of several known antibiotics. We discuss previously observed escape mechanisms and new possible therapeutic measures to combat these pathogens and further suggest caseinolytic proteins (Clp) as possible therapeutic targets to combat ESKAPE pathogens. These proteins have displayed unmatched significance in bacterial growth, viability and virulence upon chronic infection and under stressful conditions. Furthermore, several studies have showed promising results with targeting Clp proteins in bacterial species, such as Mycobacterium tuberculosis, Staphylococcus aureus and Bacillus subtilis.

The Molecular Epidemiology of Resistance to Antibiotics among Klebsiella pneumoniae Isolates in Azerbaijan, Iran

Introduction

Klebsiella pneumoniae (K. pneumoniae) is one of the leading causes of hospital-acquired and community-acquired infections in the world. This study was conducted to investigate the molecular epidemiology of drug resistance in clinical isolates of K. pneumoniae in Azerbaijan, Iran.

Materials and Methods

A total of 100 nonduplicated isolates were obtained from the different wards of Azerbaijan state hospitals, Iran, from 2019 to 2020. Antibiotic susceptibility testing was done. The DNA was extracted, and the PCR for evaluation of the resistance genes was carried out.

Results

The highest antibiotic resistance was shown to ampicillin (96%), and the highest susceptibility was shown to tigecycline (9%), and 85% of isolates were multidrug resistant. The most frequent ESBL gene in the tested isolates was bla _SHV-1 in 58%, followed by bla _CTXM-15 (55%) and bla _{SHV-11 (}42%). The qepA, oqxB, and oqxA genes were found to be 95%, 87.5%, and 70%, respectively. We detected tetB in 42%, tetA in 32%, tetD in 21%, and tetC in 16%. Seventy isolates were resistant to co-trimoxazole, and the rate of resistance genes was sul1 in 71%, followed by sul2 (43%), dfr (29%), and sul3 (7%). The most common aminoglycoside resistance genes were ant3Ia, aac6Ib, aph3Ib, and APHs in 44%, 32%, 32%, and 31.4%, respectively. The most frequent resistance gene to fosfomycin was fosA (40%) and fosX (40%) followed by fosC (20%).

Conclusion

The results of this study indicate the high frequency of drug resistance among K. pneumoniae isolated from hospitals of Azerbaijan state. The present study shows the presence of high levels of drug-resistant genes in various antibiotics, which are usually used in the treatment of infections due to K. pneumoniae.

Variation in Accessory Genes Within the Klebsiella oxytoca Species Complex Delineates Monophyletic Members and Simplifies Coherent Genotyping

Members of the Klebsiella oxytoca species complex (KoSC) are emerging human pathogens causing infections of increasing significance especially in healthcare settings. KoSC strains are affiliated with distinct phylogroups based on genetic variation at the beta-lactamase gene (bla OXY) and it has been proposed that each major phylogroup represents a unique species. However, since the typing methods applied in clinical settings cannot differentiate every species within the complex, existing clinical, epidemiological and DNA sequence data is frequently misclassified. Here we systematically examined the phylogenetic relationship of KoSC strains to evaluate robustness of existing typing methods and to provide a simple typing strategy for KoSC members that cannot be differentiated biochemically. Initial analysis of a collection of K. oxytoca, K. michiganensis, K. pasteurii, and K. grimontii strains of environmental origin showed robust correlation of core phylogeny and blaOXY grouping. Moreover, we identified species-specific accessory gene loci for these strains. Extension of species correlation using database entries initially failed. However, assessment of average nucleotide identities (ANI) and phylogenetic validations showed that nearly one third of isolates in public databases have been misidentified. Reclassification resulted in a robust reference strain set for reliable species identification of new isolates or for retyping of strains previously analyzed by multi-locus sequence typing (MLST). Finally, we show convergence of ANI, core gene phylogeny, and accessory gene content for available KoSC genomes. We conclude that also the monophyletic members K. oxytoca, K. michiganensis, K. pasteurii and K. grimontii can be simply differentiated by a PCR strategy targeting bla OXY and accessory genes defined here.

Detection of extended spectrum beta-lactamase genes in Pseudomonas aeruginosa isolated from patients in rural Eastern Cape Province, South Africa

The proliferation of extended spectrum beta-lactamase (ESBL) producing Pseudomonas aeruginosa represent a major public health threat. In this study, we evaluated the antimicrobial resistance patterns of P. aeruginosa strains and characterized the ESBLs and Metallo- β-lactamases (MBL) produced. Strains of P. aeruginosa cultured from patients who attended Nelson Mandela Academic Hospital and other clinics in the four district municipalities of the Eastern Cape between August 2017 and May 2019 were identified; antimicrobial susceptibility testing was carried out against thirteen clinically relevant antibiotics using the BioMérieux VITEK 2 and confirmed by Beckman autoSCAN-4 System. Real-time PCR was done using Roche Light Cycler 2.0 to detect the presence of ESBLs; bla_SHV, bla_TEM and bla_CTX-M genes; and MBLs; bla_IMP, bla_VIM. Strains of P. aeruginosa demonstrated resistance to wide-ranging clinically relevant antibiotics including piperacillin (64.2%), followed by aztreonam (57.8%), cefepime (51.5%), ceftazidime (51.0%), piperacillin/tazobactam (50.5%), and imipenem (46.6%). A total of 75 (36.8%) multidrug-resistant (MDR) strains were observed of the total pool of isolates. The bla_TEM, bla_SHV and bla_CTX-M was detected in 79.3%, 69.5% and 31.7% isolates (n = 82), respectively. The bla_IMP was detected in 1.25% while no bla_VIM was detected in any of the strains tested. The study showed a high rate of MDR P. aeruginosa in our setting. The vast majority of these resistant strains carried bla_TEM and bla_SHV genes. Continuous monitoring of antimicrobial resistance and strict compliance towards infection prevention and control practices are the best defence against spread of MDR P. aeruginosa.

Klebsiella oxytoca and Emerging Nosocomial Infections

Klebsiella oxytoca is rising as a significant opportunistic pathogen causing nosocomial infections in neonates as well as adults. This pathogen's prevalence varies from 2 to 24%, but outbreaks of infections due to multidrug-resistant strains can be fatal in immunocompromised individuals with comorbidities. Klebsiella oxytoca is responsible for a wide range of ailments from colitis to infective endocarditis, other than the common urinary and respiratory tract infections. The microbe's pathogenicity has been attributed to cytotoxins' production- Tilivalline and Tilimycin, in some intestinal disorders. Klebsiella oxytoca is reported to be resistant to a wide range of antibiotics. Here, we have tried to showcase a brief overview of the emergence of Klebsiella oxytoca in healthcare facilities and the nature of resistance in this species of Klebsiella.

An Evaluation of the Antibacterial Properties of Tormentic Acid Congener and Extracts From Callistemon viminalis on Selected ESKAPE Pathogens and Effects on Biofilm Formation

ESKAPE pathogens, namely, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species, are responsible for a majority of all healthcare-acquired infections (HAI). The bacteria cause nosocomial infections in immunocompromised patients. Extracts from Callistemon viminalis have been shown to have antibacterial, antifungal, and anti-inflammatory activities. Tormentic acid congener, a pentacyclic triterpene saponin, was isolated from C. viminalis leaves. This study aimed to investigate the antibacterial effects of tormentic acid congener and leaf extracts on biofilm formation by A. baumannii, S. aureus, S. pyogenes, and P. aeruginosa. The antibacterial effects were determined by the microbroth dilution method, and ciprofloxacin was used as the standard antibacterial drug. Biofilm formation and detachment assays were performed using crystal violet staining. Production of extracellular polymeric DNA and polysaccharides from biofilms was also determined. Tormentic acid congener showed time-dependent antibacterial activity against P. aeruginosa with a MIC of 100 µg/ml and caused significant protein leakage. Antibacterial activity was found when tormentic acid congener was tested against both S. aureus and P. aeruginosa. The MICs were found to be 25 µg/ml and 12.5 µg/ml for P. aeruginosa and S. aureus cells, respectively. S. pyogenes was found to be susceptible to tormentic acid congener and the hydroethanolic extract with an MIC of 100 µg/ml and 25 µg/ml, respectively. A. baumannii was found not to be susceptible to the compound or the extracts. The compound and the extracts caused a significant decrease in the biofilm extracellular polysaccharide content of S. pyogenes. The extracts and tormentic acid congener caused detachment of biofilms and decreased the release of extracellular DNA and capsular polysaccharides from biofilms of P. aeruginosa and S. aureus. Tormentic acid congener and extracts, thus, have significant antibacterial and antibiofilm activities on these selected ESKAPE bacteria and can act as source lead compounds for the development of antibacterial triterpenoids.

Extended Spectrum Beta-Lactamase-Resistant Determinants among Carbapenem-Resistant Enterobacteriaceae from Beef Cattle in the North West Province, South Africa: A Critical Assessment of Their Possible Public Health Implications

Carbapenems are considered to be the last resort antibiotics for the treatment of infections caused by extended-spectrum beta-lactamase (ESBL)-producing strains. The purpose of this study was to assess antimicrobial resistance profile of Carbapenem-resistant Enterobacteriaceae (CRE) isolated from cattle faeces and determine the presence of carbapenemase and ESBL encoding genes. A total of 233 faecal samples were collected from cattle and analysed for the presence of CRE. The CRE isolates revealed resistance phenotypes against imipenem (42%), ertapenem (35%), doripenem (30%), meropenem (28%), cefotaxime, (59.6%) aztreonam (54.3%) and cefuroxime (47.7%). Multidrug resistance phenotypes ranged from 1.4 to 27% while multi antibiotic resistance (MAR) index value ranged from 0.23 to 0.69, with an average of 0.40. Escherichia coli (E. coli), Klebsiella pneumoniae (K. pneumoniae), Proteus mirabilis (P. mirabilis) and Salmonella (34.4, 43.7, 1.3 and 4.6%, respectively) were the most frequented detected species through genus specific PCR analysis. Detection of genes encoding carbapenemase ranged from 3.3% to 35% (blaKPC, blaNDM, blaGES, blaOXA-48, blaVIM and blaOXA-23). Furthermore, CRE isolates harboured ESBL genes (blaSHV (33.1%), blaTEM (22.5%), blaCTX-M (20.5%) and blaOXA (11.3%)). In conclusion, these findings indicate that cattle harbour CRE carrying ESBL determinants and thus, proper hygiene measures must be enforced to mitigate the spread of CRE strains to food products.

Occurrence, Phenotypic and Molecular Characterization of Extended-Spectrum- and AmpC- β-Lactamase Producing Enterobacteriaceae Isolated From Selected Commercial Spinach Supply Chains in South Africa

The increasing occurrence of multidrug-resistant (MDR) extended-spectrum β-lactamase- (ESBL) and/or AmpC β-lactamase-producing Enterobacteriaceae in health care systems, the environment and fresh produce is a serious concern globally. Production practices, processing and subsequent consumption of contaminated raw fruit and vegetables represent a possible human transmission route. The purpose of this study was to determine the presence of ESBL/AmpC-producing Enterobacteriaceae in complete spinach supply chains and to characterize the isolated strains phenotypically (antimicrobial resistance profiles) and genotypically (ESBL/AmpC genetic determinants, detection of class 1, 2, and 3 integrons). Water, soil, fresh produce, and contact surface samples (n = 288) from two commercial spinach production systems were screened for ESBL/AmpC-producing Enterobacteriaceae. In total, 14.58% (42/288) of the samples were found to be contaminated after selective enrichment, plating onto chromogenic media and matrix-assisted laser desorption ionization time-of-flight mass spectrometry identity confirmation of presumptive ESBL/AmpC isolates. This included 15.28% (11/72) water and 12.12% (16/132) harvested- and processed spinach, while 25% (15/60) retail spinach samples were found to be contaminated with an increase in isolate abundance and diversity in both scenarios. Dominant species identified included Serratia fonticola (45.86%), Escherichia coli (20.83%), and Klebsiella pneumoniae (18.75%). In total, 48 (81.36%) isolates were phenotypically confirmed as ESBL/AmpC-producing Enterobacteriaceae of which 98% showed a MDR phenotype. Genotypic characterization (PCR of ESBL/AmpC resistance genes and integrons) further revealed the domination of the CTX-M Group 1 ESBL type, followed by TEM and SHV; whilst the CIT-type was the only plasmid-mediated AmpC genetic determinant detected. Integrons were detected in 79.17% (n = 38) of the confirmed ESBL/AmpC-producing isolates, of which we highlight the high prevalence of class 3 integrons, detected in 72.92% (n = 35) of the isolates, mostly in S. fonticola. Class 2 integrons were not detected in this study. This is the first report on the prevalence of ESBL/AmpC-producing Enterobacteriaceae isolated throughout commercial spinach production systems harboring class 1 and/or class 3 integrons in Gauteng Province, South Africa. The results add to the global knowledge base regarding the prevalence and characteristics of ESBL/AmpC-producing Enterobacteriaceae in fresh vegetables and the agricultural environment required for future risk analysis.

Exploring the antimicrobial resistance profiles of WHO critical priority list bacterial strains

BACKGROUND

The antimicrobial resistance of clinical, environmental and control strains of the WHO "Priority 1: Critical group" organisms, Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa to various classes of antibiotics, colistin and surfactin (biosurfactant) was determined.

METHODS

Acinetobacter baumannii was isolated from environmental samples and antibiotic resistance profiling was performed to classify the test organisms [A. baumannii (n = 6), P. aeruginosa (n = 5), E. coli (n = 7) and K. pneumoniae (n = 7)] as multidrug resistant (MDR) or extreme drug resistant (XDR). All the bacterial isolates (n = 25) were screened for colistin resistance and the mobilised colistin resistance (mcr) genes. Biosurfactants produced by Bacillus amyloliquefaciens ST34 were solvent extracted and characterised using ultra-performance liquid chromatography (UPLC) coupled to electrospray ionisation mass spectrometry (ESI-MS). The susceptibility of strains, exhibiting antibiotic and colistin resistance, to the crude surfactin extract (cell-free supernatant) was then determined.

RESULTS

Antibiotic resistance profiling classified four A. baumannii (67%), one K. pneumoniae (15%) and one P. aeruginosa (20%) isolate as XDR, with one E. coli (15%) and three K. pneumoniae (43%) strains classified as MDR. Many of the isolates [A. baumannii (25%), E. coli (80%), K. pneumoniae (100%) and P. aeruginosa (100%)] exhibited colistin resistance [minimum inhibitory concentrations (MICs) ≥ 4 mg/L]; however, only one E. coli strain isolated from a clinical environment harboured the mcr-1 gene. UPLC-MS analysis then indicated that the B. amyloliquefaciens ST34 produced C13-16 surfactin analogues, which were identified as Srf1 to Srf5. The crude surfactin extract (10.00 mg/mL) retained antimicrobial activity (100%) against the MDR, XDR and colistin resistant A. baumannii, P. aeruginosa, E. coli and K. pneumoniae strains.

CONCLUSION

Clinical, environmental and control strains of A. baumannii, P. aeruginosa, E. coli and K. pneumoniae exhibiting MDR and XDR profiles and colistin resistance, were susceptible to surfactin analogues, confirming that this lipopeptide shows promise for application in clinical settings.

Emergence of NDM-1- and CTX-M-3-Producing Raoultella ornithinolytica in Human Gut Microbiota

Raoultella ornithinolytica is an opportunistic pathogen of the Enterobacteriaceae family and has been implicated in nosocomial infections in recent years. The aim of this study was to characterize a carbapenemase-producing R. ornithinolytica isolate and three extended-spectrum β-lactamase (ESBL)-producing R. ornithinolytica isolates from stool samples of adults in a rural area of Shandong Province, China. The species were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rDNA sequence analysis. Antimicrobial susceptibility test showed that all four isolates were multidrug-resistant (MDR). The whole genome sequence (WGS) of these isolates was determined using an Illumina HiSeq platform, which revealed MDR-related genes. The S1 nuclease-pulsed-field gel electrophoresis (S1-PFGE) was used to characterize the plasmids carried by the R. ornithinolytica isolates. The bla_NDM-1 and bla_CTX-M-3 genes were probed using Southern blotting, which confirmed the location of both genes on the same plasmid with molecular weight of 336.5–398.4 kb. The transferability of bla_NDM-1 and bla_CTX-M was also confirmed by conjugation assays. Finally, BLAST analysis of both genes showed that mobile genetic elements were associated with the spread of drug resistance genes. Taken together, we report the presence of conjugative bla_NDM-1 and bla_CTX-M plasmids in R. ornithinolytica isolates from healthy humans, which indicate the possibility of inter-species transfer of drug resistance genes. To the best of our knowledge, this is the first study to isolate and characterize carbapenemase-producing R. ornithinolytica and ESBL-producing R. ornithinolytica isolates from healthy human hosts.

A review of -multidrug-resistant Enterobacteriaceae in a neonatal unit in Johannesburg, South Africa

Background

Multi-drug resistant organisms are an increasingly important cause of neonatal sepsis.

Aim

This study aimed to review neonatal sepsis caused by multi-drug resistant Enterobacteriaceae (MDRE) in neonates in Johannesburg, South Africa.

Methods

This was a cross sectional retrospective review of MDRE in neonates admitted to a tertiary neonatal unit between 1 January 2013 and 31 December 2015.

Results

There were 465 infections in 291 neonates. 68.6% were very low birth weight (< 1500 g). The median age of infection was 14.0 days. Risk factors for MDRE included prematurity (p = 0.01), lower birth weight (p = 0.04), maternal HIV infection (p = 0.02) and oxygen on day 28 (p < 0.001). The most common isolate was Klebsiella pneumoniae (66.2%). Total MDRE isolates increased from 0.39 per 1000 neonatal admissions in 2013 to 1.4 per 1000 neonatal admissions in 2015 (p < 0.001). There was an increase in carbapenem-resistant Enterobacteriaceae (CRE) from 2.6% in 2013 to 8.9% in 2015 (p = 0.06). Most of the CRE were New Delhi metallo—β lactamase- (NDM) producers.

The all-cause mortality rate was 33.3%. Birth weight (p = 0.003), necrotising enterocolitis (p < 0.001) and mechanical ventilation (p = 0.007) were significantly associated with mortality. Serratia marcescens was isolated in 55.2% of neonates that died.

Conclusions

There was a significant increase in MDRE in neonatal sepsis during the study period, with the emergence of CRE. This confirms the urgent need to intensify antimicrobial stewardship efforts and address infection control and prevention in neonatal units in LMICs. Overuse of broad- spectrum antibiotics should be prevented.

A Study of the Virulence Traits of Carbapenem-Resistant Klebsiella pneumoniae Isolates in a Galleria mellonella Model

The increasing incidence of carbapenem-resistant Klebsiella pneumoniae (CRKP) strains is considered as a terrifying public health concern. This study target was to gain a further insight into the virulence traits of CRKP isolates in Egypt. The study was carried out by using 43 clinical K. pneumoniae isolates. Antibiotic susceptibility testing, biofilm formation assay, and molecular characterization of carbapenemase and virulence genes were done for all isolates. In addition, the genotypic relationship between CRKP isolates was identified by using enterobacterial repetitive intergenic consensus-polymerase chain reactions (ERIC-PCRs). A Galleria mellonella survival assay was adopted for in vivo testing of virulence of the CRKP. Carbapenem resistance was exhibited among 58% (25/43) isolates. Minimum inhibitory concentration values of carbapenem-resistant K. pneumoniae (CRKP) ranged from 32 to 128 μg/mL. Biofilm assay has revealed that 21 isolates (49%) had moderate biofilm formation and 11 isolates (25.5%) were strong biofilm producers. Bla_NDM-1 was recognized in 20.9% (9/43) of the isolates, while bla_OXA-48 was observed in 18.5% (8/43). Type 3 fimbriae (mrkD) and entB were addressed among 72.1% and 62.8% of K. pneumoniae isolates, respectively. The ybtS and iutA genes were detected among 44.2% and 37.2% of the isolates, respectively. ERIC-PCR showed 23 genetic profiles among CRKP isolates. CRKP biofilm producers were virulent according to the G. mellonella model, which indicates the importance of biofilm as a virulence trait among CRKP. This study indicates the emergence of CRKP with increased virulence traits, especially biofilm formation, in Egypt. This alarming report highlights the ongoing need for effective screening procedures and strict infection control measures.

Whole Genome Sequencing of Extended Spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae Isolated from Hospitalized Patients in KwaZulu-Natal, South Africa

Extended spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae remain a critical clinical concern worldwide. The aim of this study was to characterize ESBL-producing K. pneumoniae detected within and between two hospitals in uMgungundlovu district, South Africa, using whole genome sequencing (WGS). An observational period prevalence study on antibiotic-resistant ESKAPE (i.e. Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.) bacteria was carried out in hospitalized patients during a two-month period in 2017. Rectal swabs and clinical specimens were collected from patients hospitalized and were screened for ESBL-producing, Gram-negative ESKAPE bacteria using cefotaxime-containing MacConkey agar and ESBL combination disk tests. Nine confirmed ESBL-K. pneumoniae isolated from six patients and two hospitals were whole genome sequenced using an Illumina MiSeq platform. Genome sequences were screened for presence of integrons, insertion sequences, plasmid replicons, CRISPR regions, resistance genes and virulence genes using different software tools. Of the 159 resistant Gram-negative isolates collected, 31 (19.50%) were ESBL-producers, of which, nine (29.03%) were ESBL-K. pneumoniae. The nine K. pneumoniae isolates harboured several β-lactamase genes, including bla_CTX-M-15, bla_TEM-1b, bla_SHV-1, bla_OXA-1 concomitantly with many other resistance genes e.g. acc(6')-lb-cr, aadAI6, oqxA and oqxB that confer resistance to aminoglycosides and/or fluoroquinolones, respectively. Three replicon plasmid types were detected in both clinical and carriage isolates, namely ColRNAI, IncFIB(K), IncF(II). Sequence type ST152 was confirmed in two patients (one carriage isolate detected on admission and one isolate implicated in infection) in one hospital. In contrast, ST983 was confirmed in a clinical and a carriage isolate of two patients in two different hospitals. Our data indicate introduction of ESBL-producing K. pneumoniae isolates into hospitals from the community. We also found evidence of nosocomial transmission within a hospital and transmission between different hospitals. The Clustered Regularly Interspaced Palindromic Repeats (CRISPR)-associated cas3 genes were further detected in two of the nine ESBL-KP isolates. This study showed that both district and tertiary hospital in uMgungundlovu District were reservoirs for several resistance determinants and highlighted the necessity to efficiently and routinely screen patients, particularly those receiving extensive antibiotic treatment and long-term hospitalization stay. It also reinforced the importance of infection, prevention and control measures to reduce the dissemination of antibiotic resistance within the hospital referral system in this district.

Occurrence, Identification, and Antimicrobial Resistance Profiles of Extended-Spectrum and AmpC β-Lactamase-Producing Enterobacteriaceae from Fresh Vegetables Retailed in Gauteng Province, South Africa

Extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase-producing Enterobacteriaceae are no longer restricted to the health care system, but represent increased risks related to environmental integrity and food safety. Fresh produce has been increasingly reported to constitute a reservoir of multidrug-resistant (MDR) potential human pathogenic Enterobacteriaceae. This study aimed to detect, identify, and characterize the antimicrobial resistance of ESBL/AmpC-producing Enterobacteriaceae isolates from fresh vegetables at point of sale. Vegetable samples (spinach, tomatoes, lettuce, cucumber, and green beans; n = 545) were purchased from retailers in Gauteng, the most densely populated province in South Africa. These included street vendors, trolley vendors, farmers' market stalls, and supermarket chain stores. Selective enrichment, plating onto chromogenic media, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) confirmation of isolate identities showed that 17.4% (95/545) vegetable samples analyzed were contaminated with presumptive ESBL/AmpC-producing Enterobacteriaceae. Dominant species identified included Escherichia coli, Enterobacter cloacae, Enterobacter asburiae, and Klebsiella pneumoniae. Phenotypic antibiotic resistance analysis showed that 96.1% of 77 selected isolates were MDR, while resistance to aminoglycoside (94.8%), chloramphenicol (85.7%), and tetracycline (53.2%) antibiotic classes was most prevalent. Positive phenotypic analysis for ESBL production was shown in 61 (79.2%) of the 77 isolates, and AmpC production in 41.6% of the isolates. PCR and sequencing confirmed the presence of β-lactamase genes in 75.3% isolates from all vegetable types analyzed, mainly in E. coli, Enterobacter spp., and Serratia spp. isolates. CTX-M group 9 (32.8%) was the dominant ESBL type, while EBC (24.1%) was the most prevalent plasmidic type AmpC β-lactamase. Our findings document for the first time the presence of MDR ESBL/AmpC-producing Enterobacteriaceae in raw vegetables sold at selected retailers in Gauteng Province, South Africa.