Antibiogram and Genetic Characterization of Carbapenem-Resistant Gram-Negative Pathogens Incriminated in Healthcare-Associated Infections

Prevalence of multidrug resistance Salmonella species isolated from clinical specimens at University of Gondar comprehensive specialized hospital Northwest Ethiopia: A retrospective study

BACKGROUND

Multidrug resistance Salmonellosis remains an important public health problem globally. The disease is among the leading causes of morbidity and mortality in developing countries, but there have been limited recent studies about the prevalence, antimicrobial resistance, and multidrug resistance patterns of Salmonella isolates from various clinical specimens.

OBJECTIVE

Aimed to assess the prevalence, antimicrobial resistance, and multidrug resistance patterns of Salmonella isolates from clinical specimens at the University of Gondar Comprehensive Specialised Hospital, northwestern Ethiopia.

METHOD

A retrospective hospital-based cross-sectional study was conducted to determine the prevalence, antimicrobial resistance, and multidrug resistance patterns of isolated from all clinical specimens at the University of Gondar Salmonella Comprehensive Specialised Hospital from June 1st, 2017 to June 3rd, 2022. A total of 26,154 data points were collected using a checklist of records of laboratory registration. Clinical specimens were collected, inoculated, and incubated for about a week with visual inspection for growth and gram staining. The isolates were grown on MacConkey agar and Xylose Lysine Deoxycholate agar. Pure colonies were identified with a conventional biochemical test, and those unidentified at the species level were further identified by the analytical profile index-20E. Then, antimicrobial susceptibility was determined by the Kirby-Bauer disc diffusion technique. The multidrug resistance Salmonella isolates was identified using the criteria set by Magiorakos. Finally, the data was cleaned and checked for completeness and then entered into SPSS version 26 for analysis. Then the results were displayed using tables and figures.

RESULTS

Of the total 26,154 Salmonella suspected clinical samples, 41 (0.16%) Salmonella species were isolated. Most of the Salmonella isolates, 19 (46.3%), were in the age group of less than 18 years, followed by the age group of 19-44 years, 11 (26.8%). In this study, S. enterica subsp. arizonae accounts for the highest 21 (51%), followed by S. paratyphi A 9 (22%). Of the Salmonella isolates, S. typhi were highly resistant to ampicillin (100%), followed by tetracycline and trimethoprim-sulfamethoxazole, each accounting for 83.3%. Furthermore, S. paratyphi A was resistant to ampicillin (100%), tetracycline (88.9%), and chloramphenicol (88.9%). The overall multi-drug resistance prevalence was 22 (53.7%; 95% CI: 39.7-61). Accordingly, S. paratyphi A was 100% multidrug-resistant, followed by S. typhi (66.6%).

CONCLUSION

A low prevalence of Salmonella species was observed in the past six years. Moreover, most S. typhi and S. paratyphi strains in the study area were found to be resistant to routinely recommended antibiotics like ciprofloxacin and ceftriaxone, compared to what was reported earlier. In addition, all isolates of S. paratyphi A and the majority of S. typhi were multidrug resistant. Therefore, health professionals should consider antimicrobial susceptibility tests and use antibiotics with caution for Salmonellosis management.

Phage Therapy, a Salvage Treatment for Multidrug-Resistant Bacteria Causing Infective Endocarditis

Infective endocarditis (IE) is defined as an infection of the endocardium, or inner surface of the heart, most frequently affecting the heart valves or implanted cardiac devices. Despite its rarity, it has a high rate of morbidity and mortality. IE generally occurs when bacteria, fungi, or other germs from another part of the body, such as the mouth, spread through the bloodstream and attach to damaged areas in the heart. The epidemiology of IE has changed as a consequence of aging and the usage of implantable cardiac devices and heart valves. The right therapeutic routes must be assessed to lower complication and fatality rates, so this requires early clinical suspicion and a fast diagnosis. It is urgently necessary to create new and efficient medicines to combat multidrug-resistant bacterial (MDR) infections because of the increasing threat of antibiotic resistance on a worldwide scale. MDR bacteria that cause IE can be treated using phages rather than antibiotics to combat MDR bacterial strains. This review will illustrate how phage therapy began and how it is considered a powerful potential candidate for the treatment of MDR bacteria that cause IE. Furthermore, it gives a brief about all reported clinical trials that demonstrated the promising effect of phage therapy in combating resistant bacterial strains that cause IE and how it will become a hope in future medicine.

Biogenic Nanoparticles Silver and Copper and Their Composites Derived from Marine Alga Ulva lactuca: Insight into the Characterizations, Antibacterial Activity, and Anti-Biofilm Formation

Bacterial pathogens cause pain and death, add significantly to the expense of healthcare globally, and pose a serious concern in many aspects of daily life. Additionally, they raise significant issues in other industries, including pharmaceuticals, clothing, and food packaging. Due to their unique properties, a great deal of attention has been given to biogenic metal nanoparticles, nanocomposites, and their applications against pathogenic bacteria. This study is focused on biogenic silver and copper nanoparticles and their composites (UL/Ag2 O-NPS, Ul/CuO-NPs, and Ul/Ag/Cu-NCMs) produced by the marine green alga Ulva lactuca. The characterization of biogenic nanoparticles UL/Ag2 O-NPS and Ul/CuO-NPs and their composites Ul/Ag/Cu-NCMs has been accomplished by FT-IR, SEM, TEM, EDS, XRD, and the zeta potential. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) experiments were conducted to prove antibacterial activity against both Gram-positive and Gram-negative bacteria and anti-biofilm. The FTIR spectroscopy results indicate the exiting band at 1633 cm-1, which represents N-H stretching in nanocomposites, with a small shift in both copper and silver nanoparticles, which is responsible for the bio-reduction of nanoparticles. The TEM image reveals that the Ul/Ag/Cu-NCMs were hexagonal, and the size distribution ranged from 10 to 35 nm. Meanwhile, Ul/CuO-NPs are rod-shaped, whereas UL/Ag2 O-NPS are spherical. The EDX analysis shows that Cu metal was present in a high weight percentage over Ag in the case of bio-Ag/Cu-NCMs. The X-ray diffraction denotes that Ul/Ag/Cu-NCMs, UL/CuO-NPs, and UL/Ag2 O-NPS were crystalline. The results predicted by the zeta potential demonstrate that Ul/Ag/Cu-NCMs were more stable than Ul/CuO-NPs. The antibacterial activity of UL/Ag2 O-NPS, Ul/Ag/Cu-NCMs, and UL/CuO-NPs was studied against eleven Gram-negative and Gram-positive multidrug-resistant bacterial species. The maximum inhibition zones were obtained with UL/Ag2 O-NPS, followed by Ul/Ag/Cu-NCMs and Ul/CuO-NPs in all the tested bacteria. The maximum anti-biofilm percentage formed by E. coli KY856933 was obtained with UL/Ag2 O-NPS. These findings suggest that the synthesized nanoparticles might be a great alternative for use as an antibacterial agent against different multidrug-resistant bacterial strains.

Molecular characterization of multidrug resistant Acinetobacter baumannii clinical isolates from Alexandria, Egypt

Carbapenem resistant Acinetobacter baumannii is a major global concern, especially in countries of the Middle East and North Africa, where the antibiotic resistance rates are on the rise. The aim of this study was to study the genomic characteristics and antimicrobial susceptibility profile of thirty-six multidrug resistant A. baumannii clinical isolates obtained in hospitals from Alexandria, Egypt. Antibiotic resistance rates were estimated by determination of Minimum Inhibitory Concentrations. Carbapenemase genes, other antibiotic resistance genes and virulence factors were then screened by the use of Whole Genome Sequencing. Isolates were also subjected to Multi Locus Sequence Typing (MLST) using the Pasteur Scheme and to core genome MLST to study their clonal relatedness. In addition, plasmid analysis was performed by the use of a commercial kit and S1- Pulsed Field Gel Electrophoresis, and Hybridization experiments with DIG-labeled DNA probes for bla NDM-1, blaPER-7 and bla GES-like were performed to locate these genes. The majority of isolates were resistant to β-lactams (including carbapenems), fluoroquinolones, aminoglycosides and trimethoprim; and some showed resistance to cefiderocol and minocycline. We identified 8 different bla OXA-51-like variants including bla OXA-51, bla OXA-64, bla OXA-65, bla OXA-66, bla OXA-68, bla OXA-91, bla OXA-94 and bla OXA-336; bla OXA-23, bla NDM-1, bla PER-7, bla GES-like and bla ADC-like and other antibiotic resistance genes, some of these genes were within transposons or class 1 integrons. Multiple virulence factors responsible for adherence, biofilm production, type II and type VI secretion systems, exotoxins, exoenzymes, immune modulation and iron uptake were observed and 34 out of 36 isolates showed motility. Thirty-five out of 36 isolates clustered with International Clones 2, 4, 5, 7, 8 and 9; and 9 STs were identified including ST570, ST2, ST600, ST15, ST113, ST613, ST85, ST158, ST164. Plasmids ranging in size from 1.7 to 70 kb were found; bla NDM-1 and blaPER-7 genes were located in the chromosome and bla GES-like genes were simultaneously located in the chromosome and in a plasmid of 70kb. In conclusion, this study revealed a wide spectrum of antibiotic resistance genes and a variety of lineages among A. baumannii isolated in hospitals from Alexandria, and highlights the importance of investigating the molecular epidemiology to control the spread of multi-drug resistant isolates.

Antimicrobial resistance and virulence genes of invasive Salmonella enterica from children with bacteremia in north-central Nigeria

Objectives

Bacteremia due to invasive Salmonella enterica has been reported earlier in children in Nigeria. This study aimed to detect the virulence and antibiotic resistance genes of invasive Salmonella enterica from children with bacteremia in north-central Nigeria.

Method

From June 2015 to June 2018, 4163 blood cultures yielded 83 Salmonella isolates. This is a secondary cross-sectional analysis of the Salmonella isolates. The Salmonella enterica were isolated and identified using standard bacteriology protocol. Biochemical identifications of the Salmonella enterica were made by Phoenix MD 50 identification system. Further identification and confirmation were done with polyvalent antisera O and invA gene. Antimicrobial susceptibility testing was done following clinical and laboratory standard institute guidelines. Resistant genes and virulence genes were determined using a real-time polymerase chain reaction.

Result

Salmonella typhi 51 (61.4%) was the most prevalent serovar, followed by Salmonella species 13 (15.7%), choleraesuis 8 (9.6%), enteritidis 6 (7.2%), and typhimurium 5 (6.1%). Fifty-one (61.4%) of 83 Salmonella enterica were typhoidal, while 32 (38.6%) were not. Sixty-five (78.3%) of the 83 Salmonella enterica isolates were resistant to ampicillin and trimethoprim-sulfamethoxazole, followed by chloramphenicol 39 (46.7%), tetracycline 41 (41.4%), piperacillin 33 (33.9%), amoxicillin-clavulanate, and streptomycin 21 (25.3%), while cephalothin was 19 (22.9%). Thirty-nine (46.9%) of the 83 Salmonella enterica isolates were multi-drug resistant, and none were extensive drug resistant or pan-drug resistant. A bla_TEM 42 (50.6%), floR 32 (38.6%), qnrA 24 (28.9%), tetB 20 (20.1%), tetA 10 (10.0%), and tetG 5 (6.0%) were the antibiotic resistance genes detected. There were perfect agreement between phenotypic and genotypic detection of antimicrobial resistance in tetracycline, ciprofloxacin, and chloramphenicol, while beta-lactam showed κ = 0.60 agreement. All of the Salmonella enterica isolates had the virulence genes invA, sopB, mgtC, and sip4D, while 33 (39.8%), 45 (51.8%), and 2 (2.4%) had ssaQ, spvC, and ljsGI-1, respectively.

Conclusion

Our findings showed multi-drug resistant Salmonella enterica in children with bacteremia in northern Nigeria. In addition, significant virulence and antimicrobial resistance genes were found in invasive Salmonella enterica in northern Nigeria. Thus, our study emphasizes the need to monitor antimicrobial resistance in Salmonella enterica from invasive sources in Nigeria and supports antibiotic prudence.

The Antibacterial Activities and Characterizations of Biosynthesized Zinc Oxide Nanoparticles, and Their Coated with Alginate Derived from Fucus vesiculosus

Zinc oxide nanoparticles have many advantages for nano-biotechnologists due to their intense biomedical applications. ZnO-NPs are used as antibacterial agents, which influence bacterial cells through the rupture of the cell membrane and the generation of reactive free radicals. Alginate is a polysaccharide of natural origin due to its excellent properties that are used in various biomedical applications. Brown algae are good sources of alginate and are used as a reducing agent in the synthesis of nanoparticles. This study aims to synthesize ZnO-NPs by using brown alga Fucus vesiculosus (Fu/ZnO-NPs) and also to extract alginate from the same alga, which is used in coating the ZnO-NPs (Fu/ZnO-Alg-NCMs). The characterizations of Fu/ZnO-NPs and Fu/ZnO-Alg-NCMs were determined by FTIR, TEM, XRD, and zeta potential. The antibacterial activities were applied against multidrug resistance bacteria of both gram-positive and negative. The results obtained in FT-TR showed there are some shifts in the peak positions of Fu/ZnO-NPs and Fu/ZnO-Alg-NCMs. The peak at 1655 cm^-1, which assigned amide I-III, is present in both Fu/ZnO-NPs and Fu-Alg-ZnO-NCMs; this band is responsible for bio-reductions and stabilization of both nanoparticles. The TEM images proved the Fu/ZnO-NPs have rod shapes with sizes ranging from 12.68 to 17.66 and are aggregated, but Fu/ZnO/Alg-NCMs are spherical in shape with sizes ranging from 12.13 to 19.77. XRD-cleared Fu/ZnO-NPs have nine sharp peaks that are considered good crystalline, but Fu/ZnO-Alg-NCMs have four broad and sharp peaks that are considered semi-crystalline. Both Fu/ZnO-NPs and Fu/ZnO-Alg-NCMs have negative charges (-1.74 and -3.56, respectively). Fu/ZnO-NPs have more antibacterial activities than Fu/ZnO/Alg-NCMs in all tested multidrug-resistant bacterial strains. Fu/ZnO/Alg-NCMs had no effect on Acinetobacter KY856930, Staphylococcus epidermidis, and Enterobacter aerogenes, whereas there was an apparent effect of ZnO-NPs against the same strains.

High Levels of Multidrug-Resistant and Beta-Lactamase-Producing Bacteria in Meat and Meat Contact Surfaces, Debre Berhan Town, Ethiopia

Background

Over the years, microbial contamination caused by foodborne bacteria has led to a significant number of food recalls, particularly for meat items that have been related to outbreaks of deadly diseases. Animals often carry Salmonella and Escherichia coli bacteria in their intestines, and these bacteria contaminate raw meat during slaughter. In addition, pathogens such as Staphylococcus aureus can contaminate meat processing equipment and utensils and spread to raw meat.

Methods

A cross-sectional study was undertaken between 30 February and 15 March 2022. Sanitary conditions of abattoir and butchers and food handlers' hygienic practices were assessed using a structured questionnaire. An equal number of meat, swabs from carcasses, knife, weighing balance and cutting board samples (24 each, 120 total) were collected from abattoir and butcher shops. The collected samples were processed for bacterial isolation, antimicrobial susceptibility testing, MDR screening and confirmation, and ESBL screening and confirmation. Finally, SPSS software version 25 was used to compile and analyze the data. Descriptive data from surveys and laboratory procedures were cross-tabulated and summarized using statistical tables and figure.

Results

A total of 76 bacteria were isolated from 120 samples. Of all bacteria isolated, S. aureus 16 (21.1%). E. coli 13 (17.1%), and S. epidermidis 12 (15.8%) were the most prevalent. The rate of bacterial contamination was high in meat 18 (23.7%), carcasses 15 (19.7%) and weighing balance 15 (19.7%), respectively. Among the isolates, 18 (23.7%) were resistant for eight and more antibiotics. While, 17 (22.4%), 7(9.2%) and 4(5.3%) of the isolates were resistant for two and three, four and five, and six and seven antibiotics, respectively. Of bacteria isolated, 51/76 (67.1%) were MDR, 23/48 (47.9%) were screened for ESBL production and 13/48 (27.1%) isolates were confirmed as ESBL producer.

Conclusion

Multidrug-resistant bacterial contamination was common in meat and meat contact surfaces, which was exacerbated by inadequate sanitation and hygiene practices.

Ceftazidime-Avibactam plus aztreonam synergistic combination tested against carbapenem-resistant Enterobacterales characterized phenotypically and genotypically: a glimmer of hope

BACKGROUND

Carbapenemase-producing Enterobacterales (CPE) show rapid global dissemination and pose a significant therapeutic challenge. This study aimed to characterize carbapenemase-producing Klebsiella spp. and Escherichia coli (E. coli) phenotypically and genotypically and evaluate the effect of ceftazidime/ avibactam plus aztreonam combination.

METHODS

A total of 219 Klebsiella species and 390 E. coli strains were isolated from clinical samples, in which 80 Klebsiella spp. and 20 E coli isolates were resistant to tested carbapenems (imipenem, ertapenem, meropenem) by disk diffusion/broth dilution method and Vitek-2 compact system. MASTDISCS Combi Carba plus discs and real time PCR were used to determine type of carbapenemase phenotypically and genotypically, respectively. Interestingly, the synergistic effect between ceftazidime-avibactam (E-test) and aztreonam (disc) was tested against the CPE isolates.

RESULTS

Out of the carbapenem-resistant isolates, 76.25% Klebsiella spp. isolates were extensively drug-resistant (XDR) while 18.75% were pan drug-resistant (PDR), and 5% were multidrug-resistant (MDR). Regarding E. coli, 5% were PDR, 20% were MDR and 75% were XDR. More than one carbapenemase gene was detected in 99% of the isolates. In comparison between MAST-Carba plus discs and PCR results, sensitivity and specificity were (85.42-97.92%) in Klebsiella spp., and (69.64-100%) in E. coli, respectively. Moreover, a strong association was detected between both test results among Klebsiella spp. (p < 0.001) and E. coli (p = 0.012) isolates. Finally, ceftazidime-avibactam and aztreonam combination showed a synergistic effect in 98.8% of Klebsiella spp. and 95% of E coli. All 16 PDR isolates showed synergy.

CONCLUSION

This synergistic effect spots the light on new therapeutics for XDR and PDR CPE.

oprL Gene Sequencing, Resistance Patterns, Virulence Genes, Quorum Sensing and Antibiotic Resistance Genes of XDR Pseudomonas aeruginosa Isolated from Broiler Chickens

Background

Pseudomonas aeruginosa is incriminated in septicemia, significant economic losses in the poultry production sector, and severe respiratory infections in humans. This study aimed to investigate the occurrence, oprL sequencing, antimicrobial resistance patterns, virulence-determinant, Quorum sensing, and antibiotic resistance genes of P. aeruginosa retrieved from broiler chickens.

Methods

Two hundred samples were collected from 120 broiler chickens from broiler farms at Ismailia Governorate, Egypt. Consequently, the bacteriological examination was conducted and the obtained P. aeruginosa strains were tested for oprL gene sequencing, antibiogram, and PCR screening of virulence, Quorum sensing, and antibiotic resistance genes.

Results

The overall prevalence of P. aeruginosa in the examined birds was 28.3%. The oprL gene sequence analysis underlined that the tested strain expressed a notable genetic identity with various P. aeruginosa strains isolated from different geographical areas in the USA, India, China, Chile, and Ghana. PCR evidenced that the obtained P. aeruginosa strains, carrying virulence-related genes: oprL, toxA, aprA, phzM, and exoS in a prevalence of 100%, 100%, 42.5%, 33.3%, and 25.9%, respectively. Moreover, the recovered P. aeruginosa strains possessed the Quorum sensing genes: lasI, lasR, rhlI, and rhlR in a prevalence of 85.2%, 85.2%, 81.5%, and 81.5%, respectively. Furthermore, 40.7% of the isolated P. aeruginosa were XDR to seven antimicrobial classes, possessing sul1, bla _TEM, tetA, bla _CTX-M, bla _OXA-1, and aadA1 genes.

Conclusion

As we can tell, this is the first report emphasizing the evolution of XDR P. aeruginosa strains from broiler chicken in Egypt, which is supposed to be a serious threat to public health. The emerging XDR P. aeruginosa in poultry frequently harbored the oprL, toxA, and aprA virulence genes, the lasI, lasR, rhlI, and rhlR Quorum sensing genes, and the sul1, bla _TEM, tetA, bla _CTXM, bla _OXA-1, and aadA1 resistance genes.

Occurrence of Multidrug-Resistant Strains of Acinetobacter spp.: An Emerging Threat for Nosocomial-Borne Infection in Najran Region, KSA

Multidrug-resistant strains are frequent causes of nosocomial infections. The majority of nosocomial infections, particularly in critical care units (ICU), have been linked to A. baumannii, which has major clinical significance. The current paper attempts to identify the potential risk and prognosis factors for acquiring an infection due to A. baumannii compared to that of other nosocomial bacteria. In our study, we employed antibiotics generally prescribed for the initial course of treatment such as colistin, meropenem, amikacin, trimethoprime-sulfamethoxazole, levofloxacin, gentamicin, ciprofloxacin, and piperacillin-tazobactam. We found that the isolated A. baumannii were resistant at a high rate to meropenem, piperacillin-tazobactam, amikacin, levofloxacin, and ciprofloxacin, while they were partially susceptible to trimethoprim-sulfamethoxazole. Our study revealed that A. baumannii was most susceptible to gentamicin and colistin at 85.8% and 92.9%, respectively, whereas the combination of colistin and trimethoprim/sulfamethoxazole was 100% active. The patients were the primary source of infection with A. baumannii, followed by inanimate objects present in the ICU and hospital premises, and then the hospital staff who were taking care of the ICU patients. Gentamicin and colistin were the most sensitive antibiotics; of the 13 tested in total, the rate of drug resistance was above 50%. The very high rate of antibiotic resistance is alarming.

Ahmed E, Battah B, Abd Ellah NH, Zanetti S, Donadu MG. Nanotechnology as a Promising Approach to Combat Multidrug Resistant Bacteria: A Comprehensive Review and Future Perspectives

The wide spread of antibiotic resistance has been alarming in recent years and poses a serious global hazard to public health as it leads to millions of deaths all over the world. The wide spread of resistance and sharing resistance genes between different types of bacteria led to emergence of multidrug resistant (MDR) microorganisms. This problem is exacerbated when microorganisms create biofilms, which can boost bacterial resistance by up to 1000-fold and increase the emergence of MDR infections. The absence of novel and potent antimicrobial compounds is linked to the rise of multidrug resistance. This has sparked international efforts to develop new and improved antimicrobial agents as well as innovative and efficient techniques for antibiotic administration and targeting. There is an evolution in nanotechnology in recent years in treatment and prevention of the biofilm formation and MDR infection. The development of nanomaterial-based therapeutics, which could overcome current pathways linked to acquired drug resistance, is a hopeful strategy for treating difficult-to-treat bacterial infections. Additionally, nanoparticles' distinct size and physical characteristics enable them to target biofilms and treat resistant pathogens. This review highlights the current advances in nanotechnology to combat MDR and biofilm infection. In addition, it provides insight on development and mechanisms of antibiotic resistance, spread of MDR and XDR infection, and development of nanoparticles and mechanisms of their antibacterial activity. Moreover, this review considers the difference between free antibiotics and nanoantibiotics, and the synergistic effect of nanoantibiotics to combat planktonic bacteria, intracellular bacteria and biofilm. Finally, we will discuss the strength and limitations of the application of nanotechnology against bacterial infection and future perspectives.

Antimicrobial Resistance Patterns, Sequence Types, Virulence and Carbapenemase Genes of Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates from a Tertiary Care Teaching Hospital in Zunyi, China

Purpose

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has seriously threatened public health worldwide. This study aimed to investigate the antimicrobial resistance patterns, sequence types (STs), virulence and carbapenemase genes of CRKP isolates from patients in Zunyi, China.

Methods

CRKP isolates were collected from the First People's Hospital of Zunyi between January 2018 and December 2020. Antimicrobial susceptibility was determined using a VITEK^®2 analyzer and confirmed using either the broth dilution method, Kirby-Bauer method, or E-test assays. Carbapenemase production was examined using a modified carbapenem inactivation method. STs of the studied isolates were determined by multilocus sequence typing, and the presence of carbapenemase and virulence genes was examined using polymerase chain reaction assays.

Results

In total, 94 CRKP isolates were collected. All studied isolates produced carbapenemase, and the most common carbapenemase gene was New Delhi metallo-β-lactamase (NDM; 72.3%), followed by Klebsiella pneumoniae carbapenemase (KPC; 24.5%), and Verona integron-encoded metallo-β-lactamase (VIM; 3.2%). Of the studied isolates, 74.3% exhibited multidrug-resistant (MDR) phenotype, and 25.7% were either pandrug-resistant (PDR) or extensively drug-resistant (XDR) phenotypes. The most prevalent sequence type was ST2407 (37.2%), followed by ST76 (21.3%) and ST11 (11.7%). The NDM gene was present in 97.1% of ST2407 isolates and 90.0% of ST76 isolates, whereas the KPC gene was present in 90.9% of ST11 isolates. The majority of the isolates carried wabG, uge, and fimH virulence genes, with prevalence rates of 94.7%, 92.6%, and 94.7%, respectively.

Conclusion

This study describes NDM-producing ST2407 and ST76, as well as KPC-producing ST11, as the major clonal types of CRKP isolates in Zunyi, China. All CRKP isolates were resistant to multiple types of antibiotics, and the majority of isolates carried carbapenemase and virulence genes. Clonal spread of NDM-producing CRKP ST2407 and ST76, and KPC-producing CRKP ST11 should be strictly monitored.

Magnitude and associated factors of bacterial urinary tract infections among paediatric patients in Arba Minch, southern Ethiopia

Bacterial urinary tract infections (UTI) commonly occur in children; if left untreated, they may result in severe consequences such as uro-sepsis and renal damage. This study aimed to determine the bacterial profile, antimicrobial susceptibility patterns and associated factors among paediatric patients suspected of urinary tract infections in Arba Minch General Hospital (AMGH). An institution-based cross-sectional study was conducted from 01 October 2020 to 31 January 2021. A convenient sampling technique was used to recruit the participants; data were collected using a pre-tested questionnaire. To quantify the bacteria (as per the Kass count, >10⁵CFU/ml), midstream urine samples were streaked onto bacteriological media. Isolates were identified by following standard procedures. The antibiotic susceptibility test was performed as per the Kirby-Bauer disc diffusion technique. Data were analyzed using SPSS software. Out of the 246 children included, 38 (15.4%) were found to be positive for significant bacteriuria. Isolates of Escherichia coli, 9/38 (23.7%), and Staphylococcus aureus, 9/38 (23.7%), were the most predominant. The majority of Gram-negative bacterial (GNB) isolates showed resistance towards amoxicillin-clavulanate (89.5%), ampicillin (84.6%), and ceftazidime (81%). Likewise, 76.9 and 76.5% of Gram-positive bacteria (GPB), respectively, had shown resistance towards co-trimoxazole and tetracycline. Multi-drug and extensively drug resistance were detected respectively in the case of 68.4 and 15.8% of the total isolates; ESBL production was found in 57.1% of GNB, whereas 55.6% of S. aureus were methicillin-resistant S. aureus (MRSA). The process of un-circumcision was significantly associated with UTI [(adjusted odds ratio= 3.578; 95% confidence interval: 1.263 - 10.13; p=0.016)].

Multidrug-Resistant Acinetobacter baumannii Infections in the United Kingdom versus Egypt: Trends and Potential Natural Products Solutions

Acinetobacter baumannii is a problematic pathogen of global concern. It causes multiple types of infection, especially among immunocompromised individuals in intensive care units. One of the most serious concerns related to this pathogen is its ability to become resistant to almost all the available antibiotics used in clinical practice. Moreover, it has a great tendency to spread this resistance at a very high rate, crossing borders and affecting healthcare settings across multiple economic levels. In this review, we trace back the reported incidences in the PubMed and the Web of Science databases of A. baumannii infections in both the United Kingdom and Egypt as two representative examples for countries of two different economic levels: high and low-middle income countries. Additionally, we compare the efforts made by researchers from both countries to find solutions to the lack of available treatments by looking into natural products reservoirs. A total of 113 studies reporting infection incidence were included, with most of them being conducted in Egypt, especially the recent ones. On the one hand, this pathogen was detected in the UK many years before it was reported in Egypt; on the other hand, the contribution of Egyptian researchers to identifying a solution using natural products is more notable than that of researchers in the UK. Tracing the prevalence of A. baumannii infections over the years showed that the infections are on the rise, especially in Egypt vs. the UK. Further concerns are linked to the spread of antibiotic resistance among the isolates collected from Egypt reaching very alarming levels. Studies conducted in the UK showed earlier inclusion of high-throughput technologies in the tracking and detection of A. baumannii and its resistance than those conducted in Egypt. Possible explanations for these variations are analyzed and discussed.

Tryptone-stabilized silver nanoparticles' potential to mitigate planktonic and biofilm growth forms of Serratia marcescens

Several microbial pathogens are capable of forming biofilms. These microbial communities pose a serious challenge to the healthcare sector as they are quite difficult to combat. Given the challenges associated with the antibiotic-based management of biofilms, the research focus has now been shifted towards finding alternate treatment strategies that can replace or complement the antibacterial properties of antibiotics. The field of nanotechnology offers several novel and revolutionary approaches to eradicate biofilm-forming microbes. In this study, we evaluated the antibacterial and antibiofilm efficacy of in-house synthesized, tryptone-stabilized silver nanoparticles (Ts-AgNPs) against the superbug Serratia marcescens. The nanoparticles were of spherical morphology with an average hydrodynamic diameter of 170 nm and considerable colloidal stability with a Zeta potential of - 24 ± 6.15 mV. Ts-AgNPs showed strong antibacterial activities with a minimum inhibitory concentration (MIC₅₀) of 2.5 µg/mL and minimum bactericidal concentration (MBC) of 12.5 µg/mL against S. marcescens. The nanoparticles altered the cell surface hydrophobicity and inhibited biofilm formation. The Ts-AgNPs were also effective in distorting pre-existing biofilms by degrading the extracellular DNA (eDNA) component of the extracellular polymeric substance (EPS) layer. Furthermore, reduction in quorum-sensing (QS)-induced virulence factors produced by S. marcescens indicated that Ts-AgNPs attenuated the QS pathway. Together, these findings suggest that Ts-AgNPs are an important anti-planktonic and antibiofilm agent that can be explored for both the prevention and treatment of infections caused by S. marcescens.

Magnitude and antimicrobial susceptibility profiles of Gram-Negative bacterial isolates among patients suspected of urinary tract infections in Arba Minch General Hospital, southern Ethiopia

The emergence of drug-resistant Gram-negative bacterial uropathogens poses a grave threat worldwide, howbeit studies on their magnitude are limited in most African countries, including Ethiopia. Therefore, measuring the extent of their drug resistance is essential for developing strategies to confine the spread. A cross-sectional study was conducted at title hospital from 01 June to 31 August 2020. Midstream urine specimens were collected and inoculated onto MacConkey agar. Positive urine cultures showing significant bacteriuria as per the Kass count (>105 CFU/mL) were further subjected to biochemical tests to identify the type of uropathogens. Antimicrobial susceptibility testing was performed by the Kirby-Bauer disk diffusion technique, and potential carbapenemase producers were phenotypically determined by the modified carbapenem inactivation method as per the CLSI guidelines. Data were analyzed using SPSS version 26; P-value <0.05 was considered statistically significant. Totally, 422 patients were included, and the majority were females (54.7%). The prevalence of carbapenem-resistant Gram-negative uropathogens was 12.9%, and 64.7% of them were carbapenemase producers. Klebsiella pneumoniae (n = 5) was the predominant carbapenemase producer, followed by Pseudomonas aeruginosa (n = 4). Consumption of antibiotics prior to six months of commencement of the study, the presence of chronic diseases and hospitalizations were statistically associated with UTI caused by carbapenem-resistant Gram-negative uropathogens. Carbapenemase producers were resistant to most of the antibiotics tested. Our findings highlight the need for periodic regional bacteriological surveillance programs to guide empirical antibiotic therapy of UTI.

Initial empirical antibiotics of non-carbapenems for ESBL-producing E. coli and K. pneumoniae bacteremia in children: a retrospective medical record review

BACKGROUND

The efficacy of non-carbapenems as an empirical antibiotic for extended-spectrum β-lactamases (ESBL)-producing Escherichia coli and Klebsiella pneumoniae bacteremia in children remains controversial. We compared clinical and microbial outcomes according to the types of empirical antibiotics for treating pediatric patients with ESBL-producing E. coli and K. pneumoniae bacteremia.

METHODS

Data from pediatric patients aged ≤ 18 years who were hospitalized with monomicrobial ESBL-producing E. coli or K. pneumoniae bacteremia at Asan Medical Center Children's Hospital, Seoul, Korea between January 2014 and May 2019 were analyzed retrospectively. The impact of empirical therapy was assessed as 30-day all-cause mortality and 2-day microbiological outcomes evaluated by the sterility of blood cultures collected on day 2 after empirical antibiotic administration. Logistic regression analysis was used to control for the effects of confounding variables.

RESULTS

A total of 53 patients with bacteremia caused by ESBL-producing E. coli (n = 29) and K. pneumoniae (n = 24) were included in this study; the median age was 3.6 years, and all had underlying comorbidities. As empirical antibiotics, 27 patients were treated with meropenem, and non-carbapenem agents were administered to 26 patients; 84.6% (22/26) were converted to carbapenem antibiotics as the definitive antibiotic by day 2 after empirical antibiotic administration. Overall, the 30-day all-cause mortality of ESBL-producing E. coli and K. pneumoniae bacteremia was 17.0% (9/53). After adjustment, there was no statistically significant association of use of a non-carbapenem agent as an empirical antibiotic with microbiological failure on day 2 and 30-day all-cause mortality [adjusted odds ratio (OR) 1.0; 95% confidence interval (CI) 0.22-4.88, and adjusted OR 0.1; 95% CI 0.01-1.56].

CONCLUSIONS

The empirical use of non-carbapenems might not be a risk factor for mortality and early microbiological outcomes in pediatric patients with ESBL-producing E. coli and K. pneumoniae BSI if early transition to appropriate antimicrobial therapy was possible.

Neonatal Sepsis: The impact of Hypervirulent Klebsiella pneumonia in a Tertiary Care Hospital

Neonatal sepsis is a blood-stream infection that affects newborns under the age of 28 days. Sepsis is common in NICUs and has a high prevalence of Klebsiella species. As a result, the study aims to find the antibiotic resistance profile, virulence factors, and the prognosis of K. pneumoniae-infected neonates. A prospective study was conducted which included 140 neonates with clinical sepsis. Characterization of Klebsiella pneumonia isolates was done by conventional methods. Drug resistance and virulence factors were detected by phenotypic methods. Genotypic methods included 16s rRNA amplification and sequencing. Detection of multidrug-resistant genes by PCR was performed. K. pneumoniae (26.9%) was the most common pathogen isolated. A high prevalence of ESBL was detected (58.8%). The prevalence of CRKP and MβL was about 29.4%, and 23.5% respectively. Two strains were Strong biofilm producers and nine isolates showed Beta hemolysis.7 strains were positive for the string test. Four strains were positive for the wcaG gene. 3 positive for magA (K1) and 2 were for gene wzy (K2). Three isolates carried blaCTX–M, four isolates harbored blaVIM, two for IMP, and one for NDM and KPC gene. K. pneumoniae isolates in the NICU increased in frequency and antibiotic resistance. It is a serious hazard to the healthcare system, and it necessitates strict infection control methods in healthcare settings, as well as antibiotic stewardship to prevent the overuse of antibiotics in neonatal sepsis.

Functional comparison of anti-restriction and anti-methylation activities of ArdA, KlcA, and KlcAHS from Klebsiella pneumoniae

Anti-restriction proteins are typically encoded by plasmids, conjugative transposons, or phages to improve their chances of entering a new bacterial host with a type I DNA restriction and modification (RM) system. The invading DNA is normally destroyed by the RM system. The anti-restriction proteins ArdA, KlcA, and their homologues are usually encoded on plasmid of carbapenemase-resistant Klebsiella pneumoniae. We found that the plasmid sequence and restriction proteins affected horizontal gene transfer, and confirmed the anti-restriction and anti-methylation activities of ArdA and KlcA during transformation and transduction. Among the three anti-restriction proteins, ArdA shows stronger anti-restriction and anti-methylation effects, and KlcAHS was weaker. KlcA shows anti-methylation only during transformation. Understanding the molecular mechanism underlying the clinical dissemination of K. pneumoniae and other clinically resistant strains from the perspective of restrictive and anti-restrictive systems will provide basic theoretical support for the prevention and control of multidrug-resistant bacteria, and new strategies for delaying or even controlling the clinical dissemination of resistant strains in the future.

Dissemination of carbapenemase-producing Enterobacterales in the community of Rawalpindi, Pakistan

Carbapenems are considered last-line beta-lactams for the treatment of infections caused by multidrug-resistant Gram-negative bacteria. However, their activity is compromised by the rising prevalence of carbapenemase-producing Enterobacterales (CPE), which are especially marked in the Indian subcontinent. In Pakistan, previous reports have warned about the possible spread of CPE in the community, but data are still partial. This study was carried out to analyse the prevalence of CPE, the genetic characterisation, and phylogenetic links among the spreading CPE in the community. In this cohort study, we collected 306 rectal swabs from patients visiting Benazir Bhutto hospital, Rawalpindi. CPEs were screened by using ertapenem-supplemented MacConkey agar. Identification was performed by using conventional biochemical tests, and genomes were sequenced using Illumina chemistry. Antibiotic resistance genes, plasmid incompatibility groups, and Escherichia coli phylogroups were determined in silico. Sequence types were determined by using MLST tool. The prevalence of CPE carriage observed was 14.4% (44/306 samples). The most common carbapenemase-encoding gene was bla-_NDM-5 (n = 58) followed by bla_NDM-1 (n = 7), bla_NDM (non-assigned variant, n = 4), bla_OXA-181 (n = 3), bla_OXA-232 (n = 3) and bla_NDM-7 (n = 1). Most of the CPE were E. coli (55/64, 86%), and the genomic analysis revealed a pauciclonal diffusion of E. coli with ST167 (n = 14), 405 (n = 10), 940 (n = 8), 648 (n = 6) and 617 (n = 5). We obtained a second sample from 94 patients during their hospital stay in whom carriage was negative at admission and found that 7 (7.4%) acquired a CPE. Our results indicate that the prevalence of CPE carriage in the Pakistani urban community was high and driven by the dissemination of some E. coli clones, with ST167 being the most frequent. The high CPE carriage in the community poses a serious public health threat and calls for implementation of adequate preventive measures.

Bacteriological Quality and Antimicrobial Susceptibility Patterns Among Raw Milk Producers and Vendors in Gomole District, Borena Zone, Southern Ethiopia

Background and Aim

Milk consumption plays a great role in the nutrition of consumers and the income of producers as well as vendors, but their bacteriological quality causes loss of those benefits. Hence, the aim of this study was to determine the bacteriological quality, associated factors and antimicrobial susceptibility pattern among raw milk of producers and vendors in Gomole district, Borena zone, South Ethiopia, from March 1 to April 30, 2019.

Methods

A cross-sectional study was conducted on 130 purposively selected study participants. Pretested structured questionnaires and observation checklists were used to collect data. Then, 15 to 20 mL of milk samples were collected from producers and vendors for laboratory analysis. Standard plate count agar and eosin methylene blue agar were used for total bacterial count and total coliform count, respectively. Bacterial isolation from poor-quality milk was performed with biochemical tests and antimicrobial susceptibility tests using Kirby Bauer’s disk diffusion method. After completeness checking, the data were analyzed by Statistical Package for the Social Sciences version 21. Chi-square (χ²) was used to analyze association factors, and a p value <0.05 was considered statistically significant.

Results

The overall means ± standard deviation of the total bacterial count (TBC) and total coliform count (TCC) were 7.75 ± 0.882 and 6.69 ± 1.545 log10 CFU/mL, respectively. The mean TBC was significantly different between producers’ and vendors’ milks t = 2.1 (P < 0.001). The proportions of raw milk TBC and TCC of poor quality were 90% and 80%, respectively. Poor hand washing practices before milking, water source and cleanliness of milk containers were associated with poor milk quality. The isolated bacteria were E. coli (30.8%), S. aureus (17.9%) and Salmonella spp. Out of the bacterial isolates, 80.4% were extensive drug resistant, 14.3% were multidrug resistant, and 5.4% were resistant against all antimicrobials used in this study.

Conclusion

Ensuring proper hygienic practices during milking, storage and transportation to reduce milk contamination.

Virulence-associated genes analysis of carbapenemase-producing Escherichia coli isolates

Carbapenem-resistant Escherichia coli has emerged as a major public health issue across the world. This study was aimed to determine the virulence content and phylogenetic groups of carbapenemase-producing E. coli isolates in southwest Iran. One hundred and fifty-two non-duplicate E. coli isolates were collected from various clinical samples. Antibiotic susceptibility and minimum inhibitory concentrations (MIC) were determined according to the Clinical and Laboratory Standards Institute (CLSI) guidelines by Kirby-Bauer disc diffusion and agar dilution methods. Phenotypic screening of carbapenemase enzymes was performed by modified Hodge test (MHT). Detection of carbapenemase genes, phylogenetic groups, and virulence-associated genes were also performed by the PCR assay. The highest and lowest resistance rates were observed against mezlocillin (70.4%) and doripenem (13.1%), respectively. Out of 28 isolates that were resistant to carbapenem antibiotics, 12 (7.9%) strains were phenotypically carbapenemase producers. The bla_OXA-48 was the predominant carbapenemase gene, detected in 58.3% of isolates, followed by bla_IMP (41.7%) and bla_NDM (8.3%). None of the isolates harbored bla_VIM and bla_KPC genes. Among the twelve carbapenemase-producing strains, urinary isolates were mostly classified into B2 (41.7%) and D (25%) phylogenetic groups, while other clinical isolates belonged to B1 (25%) and A (8.3%) groups. The frequency of virulence-associated genes was also investigated in all isolates and ranged from 6.6% for hly to 75% for fimA. The emergence of carbapenemase-producing strains is a growing concern to public health. Therefore, the proper implementation of monitoring programs is crucial for limiting their dissemination.

Bacterial Outer Membrane Permeability Increase Underlies the Bactericidal Effect of Fatty Acids From Hermetia illucens (Black Soldier Fly) Larvae Fat Against Hypermucoviscous Isolates of Klebsiella pneumoniae

Behind expensive treatments, Klebsiella pneumoniae infections account for extended hospitalization’s high mortality rates. This study aimed to evaluate the activity and mechanism of the antimicrobial action of a fatty acid-containing extract (AWME3) isolated from Hermetia illucens (HI) larvae fat against K. pneumoniae subsp. pneumoniae standard NDM-1 carbapenemase-producing ATCC BAA-2473 strain, along with a wild-type hypermucoviscous clinical isolate, strain K. pneumoniae subsp. pneumoniae KPi1627, and an environmental isolate, strain K. pneumoniae subsp. pneumoniae KPM9. We classified these strains as extensive multidrug-resistant (XDR) or multiple antibiotic-resistant (MDR) demonstrated by a susceptibility assay against 14 antibiotics belonging to ten classes of antibiotics. Antibacterial properties of fatty acids extracted from the HI larvae fat were evaluated using disk diffusion method, microdilution, minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), half of the inhibitory concentration (MIC50), and bactericidal assays. In addition, the cytotoxocity of AWME3 was tested on human HEK293 cells, and AWME3 lipid profile was determined by gas chromatography-mass spectrometry (GC-MS) analysis. For the first time, we demonstrated that the inhibition zone diameter (IZD) of fatty acid-containing extract (AWME3) of the HI larvae fat tested at 20 mg/ml was 16.52 ± 0.74 and 14.23 ± 0.35 mm against colistin-resistant KPi1627 and KPM9, respectively. It was 19.72 ± 0.51 mm against the colistin-susceptible K. pneumoniae ATCC BAA-2473 strain. The MIC and MBC were 250 μg/ml for all the tested bacteria strains, indicating the bactericidal effect of AWME3. The MIC50 values were 155.6 ± 0.009 and 160.1 ± 0.008 μg/ml against the KPi1627 and KPM9 isolates, respectively, and 149.5 ± 0.013 μg/ml against the ATCC BAA-2473 strain in the micro-dilution assay. For the first time, we demonstrated that AWME3 dose-dependently increased bacterial cell membrane permeability as determined by the relative electric conductivity (REC) of the K. pneumoniae ATCC BAA-2473 suspension, and that none of the strains did not build up resistance to extended AWME3 treatment using the antibiotic resistance assay. Cytotoxicity assay showed that AWME3 is safe for human HEK293 cells at IC₅₀ 266.1 μg/ml, while bactericidal for all the strains of bacteria at the same concentration. Free fatty acids (FFAs) and their derivatives were the significant substances among 33 compounds identified by the GC-MS analysis of AWME3. Cis-oleic and palmitoleic acids represent the most abundant unsaturated FAs (UFAs), while palmitic, lauric, stearic, and myristic acids were the most abundant saturated FAs (SFAs) of the AWME3 content. Bactericidal resistant-free AWM3 mechanism of action provides a rationale interpretations and the utility of HI larvae fat to develop natural biocidal resistance-free formulations that might be promising therapeutic against Gram-negative MDR bacteria causing nosocomial infections.

Bacterial profile and antimicrobial susceptibility patterns in cancer patients

Background

Bloodstream infections have been the leading complications in cancer patients because they are at high risk for antibiotic-resistant bacterial infections. There is increasing evidence from different parts of the world of the high prevalence of antimicrobial-resistant bacterial strains in cancer patients. The burden of the infection is high in developing countries, especially in Ethiopia. Data on bacterial profile and antimicrobial susceptibility patterns among cancer patients in Ethiopia is limited. Thus, this study aimed to determine the predominant bacterial species causing bacteremia and their antibiotic resistance pattern among cancer patients at University of Gondar comprehensive specialized hospital.

Methods

A hospital-based, cross-sectional study was conducted on 200 study participants from March to July 2021. All cancer patients who developed a fever at the time of hospital visit were included in this study, and their socio-demographic and clinical data were collected using a structured questionnaire. Blood samples (10 mL for adults and 4 mL for children) were collected from each patient, and the collected blood samples were transferred into sterile tryptic soy broth, then incubated at 37°C for 7 days. Tryptic soy broth which showed signs of growth were Gram-stained and sub-cultured on blood agar, chocolate agar, MacConkey agar, and mannitol salt agar. The inoculated plates were then aerobically incubated at 37°C for 18–24 hours and the isolates obtained were identified using standard microbiological methods. Antimicrobial susceptibility tests were done using a modified Kirby-Bauer disk diffusion technique following CLSI 2021 guidelines. Data were entered using EPI data version 4.6 and analyzed with SPSS version 20.

Results

In this study, out of 200 cancer patients included and 67.5% (135/200) of them were males. The majorities of study participants, 56% (113/200) of cancer patients were pediatrics and 26.5% (53/200) of them belong under five years of age. Out of 200 patient samples that had undergone culture, 27% (54/200) samples had bacterial growth. Gram-positive bacterial isolates were predominant, 61.1%, and S. aureus was the predominant Gram-positive isolate, (51.5.6%), followed by coagulase-negative staphylococci (48.5%). Moreover, K. pneumoniae (47%) and P. aeruginosa (29.5%) were the most common Gram-negative bacterial isolates. Among patients who had BSIs, the highest prevalence of BSIs was observed among males (66.7%), and in pediatrics cancer patients (44.2%). Pediatric study participants were more venerable to bloodstream infection (P = 0.000) compared to adult participants. Meropenem (100%), amikacin (100%), piperacillin/tazobactam (72.3%), and ceftazidime (73.5%) were effective against for Gram-negative isolates while cefoxitin (81.2%) and penicillin (70.5%) were effective for Gram-positive isolates. Additionally, most Gram-negative and Gram-positive bacterial isolates were sensitive for gentamycin (75.9%). Multidrug resistance was seen among 17.1% bacterial isolates, and MDR in Gram-negative and Gram-positive bacteria were 83.3% and 16.7%, respectively. Gram-negative bacterial isolates showed a high prevalence of MDR than Gram-positive isolates.

Conclusions and recommendation

BSI’s remains an important health problem in cancer patients, and Gram-positive bacteria were more common as etiologic agents of BSIs in cancer patients. S. aureus was the dominant bacteria followed by CoNS, K. pneumoniae, and P. aeruginosa. Multidrug-resistant isolates found in cancer patients and routine bacterial surveillance and study of their resistance patterns may guide successful antimicrobial therapy and improve the quality of care. Therefore, strict regulation of antibiotic stewardship and infection control programs should be considered in the study area.

Processed ready-to-eat (RTE) foods sold in Yenagoa Nigeria were colonized by diarrheagenic Escherichia coli which constitute a probable hazard to human health

The study aimed to recover diarrheagenic Escherichia coli strains from processed ready-to-eat (RTE) foods in Yenagoa, Nigeria and characterize them using culture-based and molecular methods. Three hundred RTE food samples were collected randomly from different food outlets between February 2021 and August 2021 and assessed for the occurrence of E. coli using standard bacteriological procedures. The virulence factor formation and antibiotic susceptibility profile of the isolates was carried out using standard microbiological procedures. Polymerase chain reaction (PCR) was used to confirm the identity of the isolates via specific primers and further used to assay the diarrheagenic determinants of the E. coli isolates. The prevalence of E. coli positive samples based on the proliferation of E. coli on Chromocult coliform agar forming purple to violet colonies was 80(26.7%). The population density of E. coli from the RTE foods ranged from 0–4.3 × 10⁴ ± 1.47 CFU/g. The recovered E. coli isolates (n = 62) were resistant to antibiotics in different proportions such as ampicillin 62(100%), aztreonam 47(75.81%) and chloramphenicol 43(69.35%). All the recovered E. coli isolates were resistant to ≥ 2 antibiotics. The multiple antibiotic-resistant index (MARI) ranged from 0.13–0.94 with 47(75.8%) of isolates having MARI >2. A total of 48(77.4%) of the isolates were multidrug-resistant (MDR). The proportion of extracellular virulence factor formation is as follows: protease 12(19.35%), curli 39(62.9%), cellulose 21(33.89%), ornithine decarboxylase 19(30.65%) and aesculin hydrolysis 14(22.58%). The overall proportion of diarrheagenic E. coli was 33/62(53.2%). The distributions of typical diarrheagenic E. coli includes: tETEC 9(14.5%), tEPEC 13(20.9%), tEAEC 6(9.7%), tEIEC 2(3.2%) and tEHEC 3(4.8%). The proportions of atypical strains include aETEC 10(16.1%), aEAEC 5(8.1%), aEPEC 1(1.6%) and aEIEC 3(4.8%). This study demonstrated that some RTE foods sold in Yenagoa, Nigeria, are contaminated and constitute a probable human health hazard. Thus, there is a need for intensive surveillance of this isolate in RTE foods variety to spot evolving AMR phenotypes and avert food-borne infections.

High prevalence of fecal carriage of Extended-spectrum beta-lactamase and carbapenemase-producing Enterobacteriaceae among food handlers at the University of Gondar, Northwest Ethiopia

Background

Fecal carriage of extended-spectrum beta-lactamase and Carbapenemase-producing Enterobacteriaceae is a potential risk for the transmission of infection with resistant strains. Understanding the burden of these resistant strains in asymptomatic people is essential to reduce the chain of infection transmission. However, data on the fecal carriage of Extended-spectrum Beta-lactamase and Carbapenemase-producing Enterobacteriaceae among food handlers were limited in developing countries especially in Ethiopia. The aim of the present study is, therefore, to assess fecal carriage rate, associated factors, and antimicrobial resistance patterns of Extended-spectrum Beta-lactamase and Carbapenemase-producing Enterobacteriaceae among food handlers at the University of Gondar Cafeterias, Northwest Ethiopia.

Materials and methods

An institution-based cross-sectional study was conducted from February to June 2021 at the University of Gondar cafeterias. A total of 290 stool samples were collected, transported using Cary Blair transport medium, and processed. All isolates were cultured and identified by using MacConkey agar, and routine biochemical tests. Antimicrobial susceptibility testing was done to each isolate following the Kirby Bauer disk diffusion method. If the zone of inhibition was ≤ 22 mm for ceftazidime, ≤25 mm for ceftriaxone, and ≤27 for cefotaxime they were considered as potential ESBL strain and selected for a further phenotypic confirmatory. Moreover, the double-disc diffusion test and the modified carbapenem inactivation method were used for confirmations of Extended-spectrum β-lactamase and Carbapenemase-producing Enterobacteriaceae respectively. If a ≥5mm difference in zone diameter for either antimicrobial agent in combination with clavulanic acid versus the zone diameter of the agent when tested alone (without B-lactamase inhibitor), was confirmed as ESBL-PE and if the zone of inhibition diameter between 6-15mm and 16- 18mm with a pinpoint colony, it was considered as carbapenem resistance Enterobacteriaceae. Data were entered using Epi-data version 4.6 and then exported to SPSS version 26 for analysis. Potential risk factors were assessed using multivariable logistic regression and a p-value less than 0.05 was considered statistically significant.

Results

Out of 290 stool samples, 63 (21.7%) and 7 (2.4%) were confirmed as Extended-spectrum β-lactamase and Carbapenemase-producing Enterobacteriaceae. The most predominant ESBL-PE was E. coli 43 (14.8%) followed by K. pneumoniae 17 (5.9%). Most of the Extended-spectrum β-lactamase and Carbapenemase-producing isolates were resistant to tetracycline, cefotaxime, ceftazidime, and ceftriaxone (100% each). In contrast, a low resistance level was recorded for Meropenem and cefoxitin. The overall Multi-drug resistant Enterobacteriaceae (MDR) was 147 (42.3%). Antibiotics usage in the last 3 months and drinking unpasteurized milk were associated with the carriage of the Extended-spectrum beta-lactamase-Producing Enterobacteriaceae.

Conclusions and recommendations

The high fecal carriage rate of Multi-drug resistance isolate, Extended-spectrum β-lactamase, and Carbapenemase-producing Enterobacteriaceae were recorded among food handlers. Therefore, this study gives signals in the spread of drug-resistant bacteria easily to the community. Hence, the need for adjusting and promotion of infection prevention measures to prevent the spread of drug-resistant bacteria should not be underestimated.

Genomic analysis of virulence factors and antimicrobial resistance of group B Streptococcus isolated from pregnant women in northeastern Mexico

Introduction

Group B Streptococcus (GBS) causes infections in women during pregnancy and puerperium and invasive infections in newborns. The genes lmb, cylE, scpB, and hvgA are involved with increased virulence of GBS, and hypervirulent clones have been identified in different regions. In addition, increasing resistance of GBS to macrolides and lincosamides has been reported, so knowing the patterns of antibiotic resistance may be necessary to prevent and treat GBS infections. This study aimed to identify virulence genes and antibiotic resistance associated with GBS colonization in pregnant women from northeastern Mexico.

Methods

Pregnant women with 35–37 weeks of gestation underwent recto-vaginal swabbing. One swab was inoculated into Todd-Hewitt broth supplemented with gentamicin and nalidixic acid, a second swab was inoculated into LIM enrichment broth, and a third swab was submerged into a transport medium. All samples were subcultured onto blood agar. After overnight incubation, suggestive colonies with or without hemolysis were analyzed to confirm GBS identification by Gram staining, catalase test, hippurate hydrolysis, CAMP test, and incubation in a chromogenic medium. We used latex agglutination to confirm and serotype GBS isolates. Antibiotic resistance patterns were assessed by Vitek 2 and disk diffusion. Periumbilical, rectal and nasopharyngeal swabs were collected from some newborns of colonized mothers. All colonized women and their newborns were followed up for three months to assess the development of disease attributable to GBS. Draft genomes of all GBS isolates were obtained by whole-genome sequencing. In addition, bioinformatic analysis to identify genes encoding capsular polysaccharides and virulence factors was performed using BRIG, while antibiotic resistance genes were identified using the CARD database.

Results

We found 17 GBS colonized women out of 1154 pregnant women (1.47%). None of the six newborns sampled were colonized, and no complications due to GBS were detected in pregnant women or newborns. Three isolates were serotype I, 5 serotype II, 3 serotype III, 4 serotype IV, and 2 serotype V. Ten distinct virulence gene profiles were identified, being scpB, lmb, fbsA, acp, PI-1, PI-2a, cylE the most common (3/14, 21%). The virulence genes identified were scpB, lmb, cylE, PI-1, fbsA, PI-2a, acp, fbsB, PI-2b, and hvgA. We identified resistance to tetracycline in 65% (11/17) of the isolates, intermediate susceptibility to clindamycin in 41% (7/17), and reduced susceptibility to ampicillin in 23.5% (4/17). The tetM gene associated to tetracyclines resistance was found in 79% (11/14) and the mel and mefA genes associated to macrolides resistance in 7% (1/14).

Conclusions

The low prevalence of colonization and the non-occurrence of mother-to-child transmission suggest that the intentional search for GBS colonization in this population is not justified. Our results also suggest that risk factors should guide the use of intrapartum antibiotic prophylaxis. The detection of strains with genes coding virulence factors means that clones with pathogenic potential circulates in this region. On the other hand, the identification of decreased susceptibility to antibiotics from different antimicrobial categories shows the importance of adequately knowing the resistance patterns to prevent and to treat GBS perinatal infection.

Whole genome sequence of pan drug-resistant clinical isolate of Acinetobacter baumannii ST1890

Acinetobacter baumannii is an opportunistic gram-negative bacteria typically attributed to hospital-associated infection. It could also become multidrug-resistant (MDR), extensively drug-resistant (XDR), and pan drug-resistant (PDR) during a short period. Although A. baumannii has been documented extensively, complete knowledge on the antibiotic-resistant mechanisms and virulence factors responsible for pathogenesis has not been entirely elucidated. This study investigated the drug resistance pattern and characterized the genomic sequence by de novo assembly of PDR A. baumannii strain VJR422, which was isolated from a catheter-sputum specimen. The results showed that the VJR422 strain was resistant to any existing antibiotics. Based on de novo assembly, whole-genome sequences showed a total genome size of 3,924,675-bp. In silico and conventional MLST analysis of sequence type (ST) of this strain was new ST by Oxford MLST scheme and designated as ST1890. Moreover, we found 10,915 genes that could be classified into 45 categories by Gene Ontology (GO) analysis. There were 1,687 genes mapped to 34 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The statistics from Clusters of Orthologous Genes (COG) annotation identified 3,189 genes of the VJR422 strain. Regarding the existence of virulence factors, a total of 59 virulence factors were identified in the genome of the VJR422 strain by virulence factors of pathogenic bacteria databases (VFDB). The drug-resistant genes were investigated by searching in the Comprehensive Antibiotic Resistance Database (CARD). The strain harbored antibiotic-resistant genes responsible for aminoglycoside, β-lactam-ring-containing drugs, erythromycin, and streptogramin resistance. We also identified resistance-nodulation-cell division (RND) and the major facilitator superfamily (MFS) associated with the antibiotic efflux pump. Overall, this study focused on A. baumannii strain VJR422 at the genomic level data, i.e., GO, COG, and KEGG. The antibiotic-resistant genotype and phenotype as well as the presence of potential virulence associated factors were investigated.

A strategy design based on antibiotic‑resistance and plasmid replicons genes of clinical Escherichia coli strains

Since antimicrobial resistance, especially β-lactam resistance genes were common in clinical Escherichia coli strains, this study had designed and developed multiplex amplification platform for rapid and accurate detection of such resistance genes in 542 clinical E. coli isolates. The obtained specimens were subjected to bacteriological examination, antimicrobial susceptibility testing, and detection of β-lactamase genes and plasmid replicons. The major virulence genes were detected by 7 groups of multiplex PCR and eight groups of multiplex PCR were designed to detect 8 different plasmid replicons including parA-parB, iteron, repA, and RNAI. It was found that most MDR isolates were co-resistant to penicillins (AMP) and fluoroquindones (LVX, CIP) and distribution of LVX and CIP resistance was significantly higher among female than male gender. RNAI (AY234375) showed the highest detection rate, followed by the iteron (J01724) and repA (M26308), indicating the relatively higher carriage rate of corresponding plasmids. Bla_OXA acquired the highest carriage rate, followed by group 2 bla_CTX-M and bla_SHV-1, indicating their prevalence among clinical E. coli. Among the β-lactamase genes, bla_OXA acquired the highest carriage rate, followed by group 2 bla_CTX-M and bla_SHV-1, indicating their prevalence among clinical E. coli. The RNAI (AY234375) showed the highest detection rate, followed by the iteron (J01724) and repA (M26308), indicating the relatively higher carriage rate of the corresponding plasmids by clinical E. coli isolates. It is shown that the developed multiplex amplification methodology is applicable to AMR detection, and such identification of plasmid replicons and β-lactamase genes may aid in the understanding of clinical E. coli isolate epidemiology.

Genetic Characterization of Antibiotic Resistant Enterobacteriaceae Isolates From Bovine Animals and the Environment in Nigeria

There is a link between antibiotic resistance in humans, livestock and the environment. This study was carried out to characterize antibiotic resistant bovine and environmental Enterobacteriaceae isolates from Edo state, Nigeria. A total of 109 consecutive isolates of Enterobacteriaceae were isolated from March–May 2015 from 150 fecal samples of healthy bovine animals from three farms at slaughter in Edo state Nigeria. Similarly, 43 Enterobacteriaceae isolates were also obtained from a total of 100 environmental samples from different sources. Isolates were recovered and identified from samples using standard microbiological techniques. Recovered isolates were pre-identified by the Microbact Gram-Negative identification system and confirmed with Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and ribosomal multilocus sequence typing (rMLST). Antibiotic susceptibility testing was carried out by Kirby-Bauer method for 14 antibiotics. Whole genome sequencing (WGS) was carried out for isolate characterization and identification of resistance determinants. Out of 109 animal and 43 environmental Enterobacteriaceae isolates, 18 (17%) and 8 (19%) isolates based on selection criteria showed antibiotic resistance and were further investigated by whole genome sequencing (WGS). Resistance genes were detected in all (100%) of the resistant bovine and environmental Enterobacteriaceae isolates. The resistance determinants included β-lactamase genes, aminoglycoside modifying enzymes, qnr genes, sulfonamide, tetracycline and trimethoprim resistance genes, respectively. Out of the 18 and 8 resistant animal and environmental isolates 3 (17%) and 2 (25%) were multidrug resistant (MDR) and had resistance determinants which included efflux genes, regulatory systems modulating antibiotic efflux and antibiotic target alteration genes. Our study shows the dissemination of antibiotic resistance especially MDR strains among Nigerian bovine and environmental Enterobacteriaceae isolates. The presence of these resistant strains in animals and the environment constitute a serious health concern indicated by the difficult treatment options of the infections caused by these organisms. To the best of our knowledge we report the first detailed genomic characterization of antibiotic resistance in bovine and environmental Enterobacteriaceae isolates for Nigeria.

Bacterial profile, antimicrobial susceptibility patterns, and associated factors of community-acquired pneumonia among adult patients in Gondar, Northwest Ethiopia: A cross-sectional study

Introduction

Community-acquired pneumonia is associated with higher morbidity, hospitalization, and mortality in adults. Likewise, antimicrobial resistance has increased in recent decades in Ethiopia. Therefore, this study was aimed to determine the bacterial isolates, their antimicrobial susceptibility patterns, and factors associated with community-acquired pneumonia among adult patients in Gondar, Northwest Ethiopia.

Materials and methods

This institutional-based cross-sectional study was conducted from April to June 2021. Sociodemographic, clinical, and other relevant data were collected using a pre-tested questionnaire. A total of 312 sputum specimens were collected using sputum cups and inoculated into blood agar, chocolate agar, mannitol salt agar, and MacConkey agar plates, which were then incubated at 37°C for 24 hours. The bacterial isolates were identified based on Gram staining, colony characteristics, and biochemical tests. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disk diffusion method. Inducible clindamycin resistance among the S. aureus isolates was detected by the D-test. Data were entered using EPI data version 4.6 and analyzed using SPSS version 20. P-value ≤ 0.05 at 95% CI was considered statistically significant.

Results

Of 312 cases, 39.4% (n = 123; 95% CI: 34.1%–44.9%) were found to have culture-confirmed pneumonia. The most common isolates were K. pneumoniae (31.0%, n = 39), S. pneumoniae (26.2%, n = 33), and S. aureus (20.6%, n = 26). The gram-positive bacteria were susceptible to chloramphenicol (100%) and clindamycin (96.6%). Gram-negative bacteria were susceptible to gentamicin (87.5%), azithromycin (87.1%), ciprofloxacin (86.6%), and ceftriaxone (79.0%) but highly resistant to ampicillin (100%), followed by tetracycline (87.1%), doxycycline (86.4%), co-trimoxazole (80.6%), and amoxicillin-clavulanic acid (79.0%). Overall, 72.2% of the isolates were multi-drug resistant to K. pneumoniae (94.9%, n = 37), E. coli (93.8%, n = 15), and S. pneumoniae (72.7%, n = 24). Only, 7.7% of S. aureus isolates showed inducible clindamycin resistance. Aging (AOR: 3.248, 95% CI: 1.001–10.545, p = 0.050), a history of pneumonia (AOR: 7.004, 95% CI: 3.591–13.658, p = 0.001), alcohol use (AOR: 6.614, 95% CI: 3.399–12.872, p < 0.001), and overcrowded living conditions (AOR: 4.348, 95% CI: 1.964–9.624, p = 0.001) were significantly associated with culture-positive sputum.

Conclusion and recommendations

This study found a high prevalence of bacteria-caused community-acquired pneumonia among adults and low susceptibility to ampicillin, tetracyclines, and amoxicillin-clavulanic acid. Therefore, culture-based bacterial identification and local antibiotic susceptibility testing should be performed regularly. Additionally, new insights into vaccine coverage against highly multi-drug resistant bacteria, particularly K. pneumoniae, are necessary.

Prevalence of common carbapenemase genes and multidrug resistance among uropathogenic Escherichia coli phylogroup B2 isolates from outpatients in Wasit Province/ Iraq

Carbapenems are the last resort antimicrobials for the treatment of extended spectrum β-lactamases (ESBLs) producing Enterobacteriaceae. Emergence of carbapenems resistant group B2 uropathogenic E. coli (UPEC) is a major concern because of their high virulence. Prevalence of these enzymes and multidrug resistance (MDR) among B2 UPEC isolates from Iraqi outpatients with acute urinary tract infection (UTI) was evaluated in this research. Urine cultures were performed and the isolates were identified biochemically. Escherichia coli isolates were tested for phylogroup reference by quadraplex PCR, then B2 isolates were detected for antimicrobial resistance by disc diffusion test and carbapenemase genes by PCR. Escherichia coli was the most prevalent among Gram-negative isolates (66.6%) and B2 was the most detected phylogroup among E. coli isolates (33.9%). Most of B2 isolates showed high resistance rates to tested antimicrobials, especially β-lactams with MDR revealed in 100% of them. Whereas, low resistance rates were noted against carbapenems, aminoglycosides and nitrofurantoin. Carbapenemase genes were detected in 76.3% of B2 isolates. Of which, blaOXA-48 was the most frequent (57.8%), followed by blaPER (47.3%), blaKPC (15.7%), blaVEB and blaVIM (10.5%, for each). Whereas, blaGES and blaIMP genes were not found. Coproduction of these genes occurred among 17 isolates. The combination of blaOXA-48 and blaPER was the most frequent (41.1%). All carbapenemase producing isolates were MDR. These results revealed high prevalence of carbapenemase genes and MDR among B2 UPEC recovered in this study. In the study area. it is strongly advised to use aminoglycosides and nitrofurantoin for empirical treatment of UPEC.

High prevalence and antimicrobial susceptibility pattern of salmonella species and extended-spectrum β-lactamase producing Escherichia coli from raw cattle meat at butcher houses in Hawassa city, Sidama regional state, Ethiopia

BACKGROUND

Food-borne diseases related to the consumption of meat and its products had public health importance worldwide. The problem became worst in Ethiopia as the result of the tradition of eating raw cattle meat. Salmonella species and Escherichia coli are important food-borne pathogens associated with meat contamination. Hence the current study aimed to assess the prevalence and antimicrobial susceptibility of Salmonella species and Extended-spectrum β-lactamase producing Escherichia coli from raw cattle meat at butcher houses in Hawassa city, Sidama regional state, Ethiopia.

METHOD

A cross-sectional study was done on the prevalence and antimicrobial susceptibility pattern of Salmonella species and Extended-spectrum β-lactamase producing E.coli from raw cattle meat at butcher houses in Hawassa city from September to December 2020. Socio-demographic data were collected using a structured questionnaire and raw cattle meat and swab samples were collected from meat cutting equipment. The collected samples transported using icebox to Hawassa University College of Medicine and Health Sciences Microbiology Laboratory for identification. Samples were grown on different culture media and antimicrobial susceptibility tests were determined by using Kirby disc diffusion method. Data were entered and analyzed into SPSS version 23. Descriptive statistics were done and P-value < 0.05 was considered as statistically significant.

RESULT

The overall prevalence of salmonella and ESBL producing E.coli among 556 samples collected from 278 butcher houses was 36 (6.47%) (95% CI: 1.68-1.79) of which 13 (2.3%) were ESBL producing E.coli and 23(4.1%) were salmonella species. Poor hand washing practice (AOR = 2.208; 95% CI: 1.249-3.904) and touching birr while selling meat (AOR = 0.75; 95% CI: (0.433-1.299) were found to be significantly associated with the prevalence of salmonella species and E.coli on cattle meat. The isolates showed moderate levels of resistance (60-70%) against Amoxicillin/ clavulanic acid and high susceptibility (85-100%) against gentamicin, cotrimoxazole, ceftazidime, and tetracycline and the overall multidrug resistance was 33.3%.

CONCLUSION

This study revealed moderately high prevalence of salmonella and E.coli due to poor hygiene and sanitation practices in the butcher shops. Furthermore, the existence of ESBL producing E.coli isolates clearly indicate the possible threat to public health. Therefore, inspection by the right agencies must be implemented in order to prevent food-borne outbreaks and antimicrobial resistance.

Proteomics-based screening and antibiotic resistance assessment of clinical and sub-clinical Brucella species: An evolution of brucellosis infection control

Brucellae are intracellular sneaky bacteria and they can elude the host's defensive mechanisms, resulting in therapeutic failure. Therefore, the goal of this investigation was to rapid identification of Brucella species collected from animals and humans in Saudi Arabia, as well as to evaluate their resistance to antibiotics. On selective media, 364 animal samples as well as 70 human blood samples were cultured. Serological and biochemical approaches were initially used to identify a total of 25 probable cultured isolates. The proteomics of Brucella species were identified using the MALDI Biotyper (MBT) system, which was subsequently verified using real-time polymerase chain reaction (real-time PCR) and microfluidic electrophoresis assays. Both Brucella melitensis (B. melitensis) and Brucella abortus (B. abortus) were tested for antimicrobial susceptibility using Kirby Bauer method and the E-test. In total, 25 samples were positive for Brucella and included 11 B. melitensis and 14 B. abortus isolates. Twenty-two out of 25 (88%) and 24/25 (96%) of Brucella strains were recognized through the Vitek 2 Compact system. While MBT was magnificently identified 100% of the strains at the species level with a score value more than or equal to 2.00. Trimethoprim-sulfamethoxazole, rifampin, ampicillin-sulbactam, and ampicillin resistance in B. melitensis was 36.36%, 31.82%, 27.27%, and 22.70%, respectively. Rifampin, trimethoprim-sulfamethoxazole, ampicillin, and ampicillin-sulbactam resistance was found in 35.71%, 32.14%, 32.14%, and 28.57% of B. abortus isolates, correspondingly. MBT confirmed by microfluidic electrophoresis is a successful approach for identifying Brucella species at the species level. The resistance of B. melitensis and B. abortus to various antibiotics should be investigated in future studies.

Carriage of distinct blaKPC-2 and blaOXA-48 plasmids in a single ST11 hypervirulent Klebsiella pneumoniae isolate in Egypt

Background

Carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) causes serious infections with significant morbidity and mortality. However, the epidemiology and transmission mechanisms of CR-hvKP and the corresponding carbapenem-resistant plasmids require further investigation. Herein, we have characterized an ST11 K. pneumoniae strain EBSI041 from the blood sample encoding both hypervirulence and carbapenem resistance phenotypes from a patient in Egypt.

Results

K. pneumoniae strain EBSI041 showed multidrug-resistance phenotypes, where it was highly resistant to almost all tested antibiotics including carbapenems. And hypervirulence phenotypes of EBSI041 was confirmed by the model of Galleria mellonella infection. Whole-genome sequencing analysis showed that the hybrid plasmid pEBSI041-1 carried a set of virulence factors rmpA, rmpA2, iucABCD and iutA, and six resistance genes aph(3′)-VI, armA, msr(E), mph(E), qnrS, and sul2. Besides, bla_OXA-48 and bla_SHV-12 were harboured in a novel conjugative IncL-type plasmid pEBSI041-2. The bla_KPC-2-carrying plasmid pEBSI041-3, a non-conjugative plasmid lacking the conjugative transfer genes, could be transferred with the help of pEBSI041-2, and the two plasmids could fuse into a new plasmid during co-transfer. Moreover, the emergence of the p16HN-263_KPC-like plasmids is likely due to the integration of pEBSI041-3 and pEBSI041-4 via IS26-mediated rearrangement.

Conclusion

To the best of our knowledge, this is the first report on the complete genome sequence of KPC-2- and OXA-48-coproducing hypervirulent K. pneumoniae from Egypt. These results give new insights into the adaptation and evolution of K. pneumoniae during nosocomial infections.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08214-9.

In vitro activities of thiazolidione derivatives combined with daptomycin against clinical Enterococcus faecium strains

Background

Previous reports have demonstrated two thiazolidione derivatives (H2-60 and H2-81) can robustly inhibit the planktonic growth and biofilm formation of S. epidermidis and S. aureus by targeting the histidine kinase YycG. Whereas the antibacterial and anti-biofilm activity of these two thiazolidione derivatives (H2-60 and H2-81) against Enterococcus faecium remains elusive. Here, the pET28a-YycG recombinant plasmid were in vitro expressed in E. coli competent cell BL21 (DE3) and induced to express YycG’ protein (conding HisKA and HATPase_c domain) by 0.5 mM IPTG and was purified by Ni – NTA agarose and then for the autophosphorylation test. Antimicrobial testing and time-killing assay were also be determined. Anti-biofilm activity of two derivatives with sub-MIC concentration towards positive biofilm producers of clinical E. faecium were detected using polystyrene microtiter plate and CLSM.

Results

The MICs of H2-60 and H2-81 in the clinical isolates of E. faecium were in the range from 3.125 mg/L to 25 mg/L. Moreover, either H2-60 or H2-81 showed the excellent bactericidal activity against E. faecium with monotherapy or its combination with daptomycin by time-killing assay. E. faecium planktonic cells can be decreased by H2-60 or H2-81 for more than 3 × log10 CFU/mL after 24 h treatment when combined with daptomycin. Furthermore, over 90% of E. faecium biofilm formation could markedly be inhibited by H2-60 and H2-81 at 1/4 × MIC value. In addition, the frequency of the eradicated viable cells embedded in mature biofilm were evaluated by the confocal laser microscopy, suggesting that of H2-60 combined with ampicillin or daptomycin was significantly high when compared with single treatment (78.17 and 74.48% vs. 41.59%, respectively, P < 0.01).

Conclusion

These two thiazolidione derivatives (H2-60 and H2-81) could directly impact the kinase phosphoration activity of YycG of E. faecium. H2-60 combined with daptomycin exhibit the excellent antibacterial and anti-biofilm activity against E. faecium by targeting YycG.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02423-8.

Effect of Antibiotic Exposure on Upper Respiratory Tract Bacterial Flora

Background

The human microbiota modulates the immune system and forms the surface flora. Antibiotic administration causes dysbiosis in the intestinal flora. It is not clear if antibiotic administration in the community effects the upper airway flora in the mid-term or long-term. This study aims to define long-term influence of antibiotics on upper airway flora.

Material/Methods

In this prospective study, aerobic microbiological analysis of nasal and nasopharyngeal surfaces was performed. Antibiotic administration history of the last 6 months was retrieved using the social insurance database. Culture results of antibiotic-treated and antibiotic-naïve subjects were compared by Pearson’s chi-square test or Fisher’s exact test.

Results

A total of 210 subjects were included in the study. Normal flora were documented in 86 nasal swabs and 99 nasopharyngeal swabs. Most of the remaining cases demonstrated gram-positive bacterial overgrowth. There were 113 subjects who did not receive any antibiotic, and 93% of the remaining 97 patients received broad-spectrum antibiotics. Statistical analysis showed that nasal and nasopharyngeal flora did not change upon antibiotic administration, but antibiotic administration during the last month caused increased methicillin resistance development of coagulase-negative Staphylococcus and Staphylococcus aureus microorganisms.

Conclusions

Antibiotic exposure did not lead to perturbations in general composition of upper airway flora within 6 months, although the incidence of methicillin resistance in coagulase-positive and -negative Staphylococci demonstrated significant increases when patients received antibiotic during the last month. This should be considered in case of broad-spectrum antibiotic administration, since methicillin resistance increases the morbidity and mortality of nosocomial Staphylococcus infections.

High prevalence of plasmid-mediated quinolone resistance (PMQR) among E. coli from aquatic environments in Bangladesh

Fluro(quinolones) is an important class of antibiotic used widely in both human and veterinary medicine. Resistance to fluro(quinolones) can be acquired by either chromosomal point mutations or plasmid-mediated quinolone resistance (PMQR). There is a lack of studies on the prevalence of PMQR in organisms from environmental sources in Bangladesh. In this study, we investigated the occurrence of PMQR genes in E. coli from various water sources and analysed associations between multi-drug resistance (MDR) and resistance to extended spectrum β-lactam antibiotics. We analysed 300 E. coli isolates from wastewaters of urban live-bird markets (n = 74) and rural households (n = 80), rural ponds (n = 71) and river water samples (n = 75) during 2017–2018. We isolated E. coli by filtering 100 ml of water samples through a 0.2μm cellulose membrane and incubating on mTEC agar media followed by identification of isolated colonies using biochemical tests. We selected one isolate per sample for detection of PMQR genes by multiplex PCR and tested for antibiotic susceptibility by disc diffusion. Clonal relatedness of PMQR-positive isolates was evaluated by enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR). About 66% (n = 199) of E. coli isolates harbored PMQR-genes, predominantly qnrS (82%, n = 164) followed by aac(6’)-lb-cr (9%, n = 17), oqxAB (7%, n = 13), qnrB (6%, n = 11) and qepA (4%, n = 8). Around 68% (n = 135) of PMQR-positive isolates were MDR and 92% (n = 183) were extended spectrum β-lactamase (ESBL)-producing of which the proportion of positive samples was 87% (n = 159) for bla_CTX-M-1’ 34% (n = 62) for bla_TEM, 9% (n = 16) for bla_OXA-1,bla_OXA-47 and bla_CMY-2, and 2% (n = 4) for bla_SHV. Further, 16% (n = 32) of PMQR-positive isolates were resistant to carbapenems of which 20 isolates carried bla_NDM-1. Class 1 integron (int1) was found in 36% (n = 72) of PMQR-positive E. coli isolates. PMQR genes were significantly associated with ESBL phenotypes (p≤0.001). The presence of several PMQR genes were positively associated with ESBL and carbapenemase encoding genes such as qnrS with bla_CTXM-1 (p<0.001), qnrB with bla_TEM (p<0.001) and bla_OXA-1 (p = 0.005), oqxAB and aac(6’)-lb-cr with bla_SHV and bla_OXA-1 (p<0.001), qnrB with bla_NDM-1 (p<0.001), aac(6’)-lb-cr with bla_OXA-47 (p<0.001) and bla_NDM-1 (p = 0.002). Further, int1 was found to correlate with qnrB (p<0.001) and qepA (p = 0.011). ERIC-PCR profiles allowed identification of 84 of 199 isolates with 85% matching profiles which were further grouped into 33 clusters. Only 5 clusters had isolates (n = 11) with identical ERIC-PCR profiles suggesting that PMQR-positive E. coli isolates are genetically heterogeneous. Overall, PMQR-positive MDR E. coli were widely distributed in aquatic environments of Bangladesh indicating poor wastewater treatment and highlighting the risk of transmission to humans and animals.

Epidemiology and Drug Resistance of Pathogens Isolated from Cerebrospinal Fluids at a Children's Medical Center in Eastern China During 2006-2020

Objective

To investigate the epidemiology and drug resistance of pathogens isolated from cerebrospinal fluid samples at a children's medical center in eastern China and provide the basis for anti-infection treatments.

Methods

In all, 307 non-duplicated strains of pathogens were isolated from cerebrospinal fluid samples in the Children's Hospital of Soochow University from January 2006 to December 2020. Mass spectrometry was used for pathogen identification. The VITEK 2 Compact system and Kirby-Bauer method were applied to determine antimicrobial susceptibility.

Results

Among the 307 isolates, gram-positive bacteria, gram-negative bacteria and fungi accounted for 60.26%, 34.53%, and 5.21%, respectively. The most prevalent pathogens were Streptococcus pneumoniae (26.06%), Escherichia coli (20.20%) and Streptococcus agalactiae (17.26%). The number of isolates was highest in winter. The most prevalent gram-positive bacterium in children <6 months old was Streptococcus agalactiae, while Streptococcus pneumoniae was the most in children were >6 months old. The drug resistance of gram-positive bacteria, fungi and Haemophilus influenza were not high. In addition, 35 strains of gram-negative bacteria produced extended-spectrum β-lactamases (ESBLs) and 6 strains were identified as multidrug-resistant (MDR) bacteria. These strains showed much higher resistance to the antibiotics than other strains.

Conclusion

Cases of meningitis among children have increased in the past 15 years and MDR bacteria were also identified. The emergence of MDR bacteria is a cause for great concern and requires further investigation.

Design SMAP29-LysPA26 as a Highly Efficient Artilysin against Pseudomonas aeruginosa with Bactericidal and Antibiofilm Activity

Antimicrobial resistance (AMR) is a major issue to global health. The multidrug-resistant (MDR) Gram-negative infections, particularly infected by carbapenem-resistant pathogens, urgently need efficient antibiotics and novel therapy. However, the scientific challenges of aiming for innovative approaches against Gram-negative bacteria have hindered the research and development of antibiotic drugs. Phage-derived endolysins are bacteriolytic and specific for a bacterial species or genus, providing a promising antibiotic strategy. However, the outer membrane of Gram-negative bacteria could prevent the peptidoglycan layer from the hydrolysis of endolysins. Antimicrobial peptides usually destabilize the outer membrane and could enhance the antibiotic activity of endolysins. In this study, we designed new artilysins with antimicrobial-peptide SMAP29 fusion at the N-terminal of LysPA26 (named as AL-3AA, AL-9AA, and AL-15AA), and evaluated them. The results showed artilysin AL-3AA to be highly bactericidal; even 0.05 mg/mL AL-3AA could reduce 5.81 log units P. aeruginosa without EDTA in 60 min. It killed P. aeruginosa rapidly and dose-dependently through cell lysis. AL-3AA inhibited P. aeruginosa PAO1 biofilm formation and significantly decreased mature P. aeruginosa biofilms. It also had potential broad-spectrum activity against susceptible Gram-negative bacteria in the hospital, including K. pneumoniae and E. coli. The antibacterial mechanism investigation has provided valuable information about the antibacterial action of AL-3AA, which can lyse and disintegrate the bacterial quickly. These results suggested AL-3AA could be a new and promising antimicrobial agent for the combat of P. aeruginosa. IMPORTANCE Antimicrobial resistance (AMR) is a major issue to global health, particularly the multidrug-resistant (MDR) Gram-negative infections, which pose great challenges. Even new antibiotics research is ongoing, antibiotics used to treat Gram-negative bacteria in the clinical are limited in a small set of molecular scaffolds, and biomolecular categories of antibiotics are urgently needed. In this study, we designed new proteins by combining antimicrobial peptides and endolysins for synergistic bactericidal effects. One of designed proteins, named AL-3AA, showed highly bactericidal, and killed P. aeruginosa rapidly and dose-dependently through cell lysis. It also killed Klebsiella pneumoniae and Escherichia coli, showing potential broad-spectrum activity against susceptible Gram-negative bacteria in the hospital. All results suggest AL-3AA could be a new and promising antimicrobial agent for the combat of P. aeruginosa.

Migratory wild birds carrying multidrug-resistant Escherichia coli as potential transmitters of antimicrobial resistance in China

Migratory birds play an important role in the spread of multidrug-resistant (MDR) bacteria. To investigate the prevalence of MDR Escherichia coli in migratory birds in China and potential relationships with the environment, a total of 1387 samples (fecal samples, cloacal swabs, or throat swabs) were collected from migratory birds from three different river basins in China. The collected samples were processed and subjected to bacteriological examinations. Antimicrobial susceptibility testing of the recovered isolates was performed using the E-test for the detection of minimum inhibitory concentrations (MICs). Some antibiotic resistance genes were detected and the PCR products were confirmed by sequencing. In total, 478 (34.7%) E. coli isolates were recovered. The results showed that the drug-resistant E. coli isolates were highly resistant to β-lactams (43.7%) and tetracycline (22.6%), and 73 (15.3%) were MDR, including eight that were extended spectrum β-lactamase-positive. The retrieved strains harbored the bla_CTX-M, bla_TEM-1, tet(A), tet(B), tet(M), sul1, sul2, sul3, cmlA, floR, and intI1 genes with a prevalence of 5.9%, 36.4%, 80.5%, 11.9%, 6.8%, 6.8%, 47.5%, 12.7%, 50.8%, 37.3%, and 61.0%, respectively. The drug resistance rate of the isolates from southern China was higher than those from northern China. The E. coli samples collected for migratory birds in the Pearl River Basin had the highest proportion (46.7%) MDR isolates. Furthermore, MDR bacteria carried by migratory birds were closely related to the antibiotic content in the basin, which confirms that MDR bacteria carried by migratory birds are likely acquired from the environment. This study also confirmed that migratory birds are potential transmitters of MDR bacteria, demonstrating the need to reduce the use and emission of antibiotics and further in-depth studies on the mechanisms underlying drug resistance of bacteria.

Phenotypic characterization of carbapenem non-susceptible gram-negative bacilli isolated from clinical specimens

Background

Multidrug resistant, extremely drug-resistant, pan-drug resistant, carbapenem-resistant, and carbapenemase-producing gram-negative bacteria are becoming more common in health care settings and are posing a growing threat to public health.

Objective

The study was aimed to detect and phenotypically characterize carbapenem no- susceptible gram-negative bacilli at the Ethiopian Public Health Institute.

Materials and methods

A prospective cross-sectional study was conducted from June 30, 2019, to May 30, 2020, at the national reference laboratory of the Ethiopian Public Health Institute. Clinical samples were collected, inoculated, and incubated for each sample in accordance with standard protocol. Antimicrobial susceptibility testing was conducted using Kirby-Bauer disk diffusion method. Identification was done using the traditional biochemical method. Multidrug-resistant and extensively drug-resistant isolates were classified using a standardized definition established by the European Centre for Disease Prevention and Control and the United States Centers for Disease Prevention and Control. Gram-negative organisms with reduced susceptibility to carbapenem antibiotics were considered candidate carbapenemase producers and subjected to modified carbapenem inactivation and simplified carbapenem inactivation methods. Meropenem with EDTA was used to differentiate metallo-β-lactamase (MBL) from serine carbapenemase. Meropenem (MRP)/meropenem + phenylboronic acid (MBO) were used to differentiate Klebsiella pneumoniae carbapenemase (KPC) from other serine carbapenemase producing gram-negative organisms.

Results

A total of 1,337 clinical specimens were analyzed, of which 429 gram-negative bacterial isolates were recovered. Out of 429 isolates, 319, 74, and 36 were Enterobacterales, Acinetobacter species, and Pseudomonas aeruginosa respectively. In our study, the prevalence of multidrug-resistant, extensively drug-resistant, carbapenemase-producing, and carbapenem nonsusceptible gram-negative bacilli were 45.2%, 7.7%, 5.4%, and 15.4% respectively. Out of 429 isolates, 66 demonstrated reduced susceptibility to the antibiotics meropenem and imipenem. These isolates were tested for carbapenemase production of which 34.8% (23/66) were carbapenemase producers. Out of 23 carbapenemase positive gram-negative bacteria, ten (10) and thirteen (13) were metallo-beta-lactamase and serine carbapenemase respectively. Three of 13 serine carbapenemase positive organisms were Klebsiella pneumoniae carbapenemase.

Conclusion

This study revealed an alarming level of antimicrobial resistance (AMR), with a high prevalence of multidrug-resistant (MDR) and extremely drug-resistant, carbapenemase-producing gram-negative bacteria, particularly among intensive care unit patients at the health facility level. These findings point to a scenario in which clinical management of infected patients becomes increasingly difficult and necessitates the use of “last-resort” antimicrobials likely exacerbating the magnitude of the global AMR crisis. This mandates robust AMR monitoring and an infection prevention and control program.

Bacterial uropathogens and burden of antimicrobial resistance pattern in urine specimens referred to Ethiopian Public Health Institute

Background

Urinary tract infections (UTIs) are the leading causes of morbidity in the general population, and is the second most common infectious disease after respiratory infections. Appropriate antibiotic therapy is essential to achieving good therapeutic results. Therefore, the purpose of this study was to investigate the profile of pathogens cultured from urinary tract infections and to determine their resistance profiles to commonly prescribed antibiotics.

Method

A cross-sectional study was carried out at the National Referral Laboratory of the Ethiopian Institute of Public Health from January 2017 to December 2018. All positive cultures were characterized by colony morphology, Gram stain, and standard biochemical tests. The antimicrobial susceptibility test of the isolate was performed using the Kirby- Bauer disk diffusion test on Muller-Hinton agar. In addition, bacterial identification, antimicrobial susceptibility testing and phenotypic detection of MDR were performed with VITEK 2 Compact according to the manufacturer’s instructions.

Result

Out of 1012 cultured urine specimens, 325 (32.1%) was showed significant bacteriuria. The overall prevalence of UTIs was 325(32.1%) and the highest prevalence rate was obtained from 21–30 years age group 73(22.5%). Among UTIs patients, 583(57.6%) were females and 429(42.4%) were males. The UTIs of 179 (55%) women is relatively higher than that of men 146 (45%). Among 325 isolates, Gram-negative bacteria (GNB) appeared more frequently 252 (51.7%) than Gram-positive bacteria 63 (19.4%).

In GNB, E. coli 168(66.7%), Klebsiella species 32(12.7%), and Enterobacter species 13 (5.2%) were dominated isolates whereas in GPB accounted for coagulase-negative staphylococcus (CoNS) 33(52.4%), Enterococcus species 16(25.4%), and Staphylococcus aureus 10(15.9%). Major of the isolates showed high levels of antibiotic resistance to commonly prescribed antimicrobials. Imipenem, Amikacin, and Nitrofurantoin were the most sensitive antibiotics for Gram-negative isolates while Nitrofurantoin, clindamycin, and Gentamycin were effective against gram-positive uropathogens. Overall, 156/256(60.9%), 56/256(22.4%), 10/256(4%) of gram-negative isolates were MDR, XDR, and PDR respectively while among the GPB isolates, 34/63(53.1%), 10/63(15.8%), and 1/63(1.6%) were MDR, XDR, and PDR isolates respectively. Among the tested bacterial strains, 190/319 (59.5%) were MDR, 66/319 (20.7%) strains were XDR, and 11/319 (3.45%) were PDR isolated.

Conclusion

The prevalence of urinary tract infection was high, and Gram-negative organisms were the most common causes of UTIs in this study. It was found that the resistance to commonly used antibiotics is very high. Early detection and close monitoring of MDR, XDR, or even PDR bacterial strains must be started by all clinical microbiology laboratories to reduce the menace of antimicrobial resistance that is now a global problem.

In Vitro Antimicrobial Activity of Medicinal Plant Extracts against Some Bacterial Pathogens Isolated from Raw and Processed Meat

Background and aim: The poultry meat and its products are considered ideal media for bacterial growth and spoilage, as they are highly nutritive with a favorable pH. The food industry has focused its attention on a great diversity of plant species as food preservatives. The aim of this study was to investigate the presence of Staphylococcus aureus, Escherichia coli O157: H7, and Klebsiella pneumonia in food samples and to evaluate of the antibacterial activity of some medicinal plant extracts against these bacteria. Methods: Raw and processed meat samples (n = 60) were collected from abattoirs and local markets. S. aureus, E. coli O157: H7, and K. pneumonia were isolated, identified by phenotypic methods, and then confirmed by 16S rRNA gene sequencing. The antibacterial activity and spectrum of essential oils and spices powder of cumin, black seeds, cloves, cinnamon, and marjoram was determined against the isolated strains in this study by microbial count and well-diffusion techniques. Results: A total of 33 isolates have been identified as S. aureus, 30 isolates were identified as E. coli O157: H7, and 15 isolates were identified as K. pneumonia. S. aureus, E. coli O157: H7, and K. pneumonia could be detected in both fresh and processed food with higher prevalence in the processed meat. There was a significant decrease in microbial count in treated samples either with the spices powder or essential oils of the tested medicinal plants compared to control samples during storage time period. Furthermore, while the microbial count increased in the control samples, the microbial count decreased to reach zero in almost all treated samples with essential oils after 15 days of storage. Conclusion: S. aureus, E. coli O157: H7, and K. pneumonia are associated with food from animal sources, in either fresh or processed meat samples. The prevalence of them was higher in the processed meat than in fresh meat. The essential oils and spices powder of cumin, black seeds, cloves, cinnamon, and marjoram have an in vitro wide spectrum antibacterial activity with the highest antibacterial activity for the black seeds.

Prevalence and characterisation of carbapenemase encoding genes in multidrug-resistant Gram-negative bacilli

Background

Emerging worldwide in the past decade, there has been a significant increase in multidrug-resistant bacteria from serious nosocomial infections, especially carbapenemase-producing Gram-negative bacilli that have emerged worldwide. The objective of this study is to investigate carbapenem resistance in Gram-negative bacilli bacteria using phenotypic detection, antimicrobial resistance profiles and genotypic characterisation methods.

Methods

200 Gram-negative bacilli isolates were collected from different clinical specimens. All clinical samples were exposed to isolation and identification of significant pathogens applying bacteriological examination and an automated Vitek-2 system. The isolates were subjected to susceptibility tests by the Vitek-2 automated system and those isolates that were resistant to beta-lactam drugs, including carbapenems, third-generation cephalosporines or cefoxitin, were selected for phenotyping using Carba plus disc system assay for detection of carbapenemase-producing isolates. These isolates were further confirmed by molecular detection. PCR was used for the detection carbapenem-resistant genes (OXA-48, IMP, NDM, VIM, and KPC).

Results

110 (55%) of 200 Gram-negative bacilli were identified as beta-lactam-resistant isolates. The frequency of carbapenem-resistant isolates was calculated to be 30.9% (n = 34/110). A collection totalling 65/110 (59%) isolates were identified as carbapenemase producers by phenotypic method. Moreover, among the 65 carbapenemase-producing Gram-negative isolates with a positive phenotype-based result, 30 (46%), 20 (30%) and 18 (27%) isolates were positive for OXA-48, KPC and MBL enzymes, respectively, as well as the production of 27% of AmpC with porin loss. Tigecycline was the most effective antibiotic that affected 70% of MDR isolates, but high rates of resistance were detected to other tested antimicrobials. Of interest, a high incidence of MDR, XDR and PDR profiles were observed among all carbapenemase-producing isolates. 36% (24/65) of the tested isolates were MDR to 3 to 5 antimicrobial classes. 29% (17/65) of the recovered isolates were XDR to 6 to 7 antimicrobial classes. Alarmingly, 24% (16/65) of isolates displayed PDR to all the tested 8 antimicrobial classes. Genotype assay, including 53 phenotypically confirmed carbapenemase-producing isolates of Gram-negative bacilli, found 51(96%) isolates were harbouring one or more genes. The most common carbapenemase gene was bla_NDM 83% (44/53) followed by bla_OXA-48 75% (40/53), bla_VIM 49% (26/53) and bla_IMP 43% (23/53), while the gene bla_KPC was least frequent 7% (4/53). 92% (46/51) of isolates were involved in the production of more than one carbapenemase gene.

Conclusion

This study demonstrated the emergence of carbapenemase-producing Gram-negative pathogens implicated in healthcare-related infections. Accurate identification of carbapenem-resistant bacterial pathogens is essential for patient treatment, as well as the development of appropriate contamination control measures to limit the rapid spread of pathogens. Tigecycline exhibited potent antimicrobial activity against MDR, XDR and PDR-producing strains that establish a threatening alert which indicates the complex therapy of infections caused by these pathogens.