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Background: Proteus mirabilis is a Gram-negative, rod-shaped bacterium widely found in natural environments. It is known for causing a range of severe illnesses in mammals, particularly urinary tract infections (UTIs). This study evaluates the therapeutic efficacy of phage P2-71 against Proteus mirabilis in vivo and in vitro environments. Methods: The in vitro therapeutic potential of bacteriophage P2-71 was assessed through the ability of phage to kill Proteus mirabilis by using a plate counting assay, and biofilm inhibition and biofilm lysis assays using a microtitre plate method. Additionally, an in vivo UTI model in C57BL/6Jmice was developed via urethral inoculation of the bacterium. Phage therapy was administered through urethral injection over a period of 5 days. Therapeutic outcomes were measured by analyzing bacterial load, phage titer, inflammatory markers, and histopathological changes in the urine, urogenital tissues, and spleen. Results: In vitro, bacteriophage P2-71 achieved significant reductions in P. mirabilis concentrations, with log reductions of 1.537 and 0.7009 CFU/mL in laboratory and urine environments, respectively (p < 0.001). The phage also decreased biofilm formation by 34-49% and lysed 15-25% of mature biofilms at various multiplicities of infection (MOIs) (p < 0.001). In vivo, phage treatment significantly lowered bacterial concentrations in the urine on Days 1 and 3 (p < 0.0001), achieving a maximum reduction of 4.602 log10 CFU/mL; however, its effectiveness diminished by Day 5 (p > 0.05). Concurrently, phage titers decreased over time. Importantly, phage treatment notably reduced bacterial load in the bladder, kidneys, and spleen (p < 0.001). Inflammatory markers such as IL-6, IL-1β, and TNF-α were significantly lower in the treatment group, especially in the bladder (p < 0.0001), indicating an effective reduction in inflammation. Histopathological analysis showed significant mitigation of tissue damage. Conclusion: The results demonstrated that bacteriophage P2-71 is a promising alternative therapy for UTIs caused by MDR Proteus mirabilis. This bacteriophage therapy offers a viable strategy for managing infections where traditional antimicrobials fail, highlighting its potential in clinical applications. [ABSTRACT FROM AUTHOR]

Introduction: Multidrug-resistant tuberculosis (MDR-TB) remains a challenge in the TB program of Taiwan, where 0.5% of new cases and 2.1% of previously treated cases were resistant to at least rifampin (RIF) and isoniazid (INH). Since >80% of our MDR-TB are new cases, genotyping of MDR Mycobacterium tuberculosis is implemented to facilitate contact investigation, cluster identification, and outbreak delineation. Methods: This is a population-based retrospective cohort study analyzing MDR-TB cases from 2019 to 2022. Whole genome sequencing (WGS) was performed using the Illumina MiSeq and analyzed using the TB Profiler. A single nucleotide polymorphism (SNP) threshold of =12 and phylogenetic methods were used to identify putative transmission clusters. An outbreak was confirmed using genomic data and epidemiologic links. Results: Of the 297 MDR-TB cases, 246 (82.8%), 45 (15.2%), and 6 (2.0%) were simple MDR, extensively drug-resistant tuberculosis (pre-XDR-TB) and extensively drug-resistant tuberculosis (XDR-TB), respectively. The sublineage 2.2 modern Beijing was the predominant (48.8%) MDR-TB strain in Taiwan. Phylogenetic analysis identified 25.3% isolates in 20 clusters, with cluster sizes ranging from 2 to 13 isolates. Nevertheless, only 2 clusters, one household and one community, were confirmed as outbreaks. In this study, we found that males had a higher risk of MDR-TB transmission compared to females, and those infected with the sublineage 2.1-proto-Beijing genotype isolates were at a higher risk of transmission. Furthermore, 161 (54.2%) isolates harbored compensatory mutations in the rpoC and non-rifampicin resistant determinant region (non-RRDR) of the rpoB gene. MDR-TB strains containing rpoB S450L and other compensatory mutations concurrently were significantly associated with clusters, especially the proto-Beijing genotype strains with the compensatory mutation rpoC E750D or the modern Beijing genotype strains with rpoC D485Y/rpoC E1140D. Discussion: Routine and continuous surveillance using WGS-based analysis is recommended to warn of risks and delineate transmission clusters of MDR-TB. We proposed the use of compensatory mutations as epidemiological markers of M. tuberculosis to interrupt putative MDR-TB transmission. [ABSTRACT FROM AUTHOR]

Introduction: The global increase of multidrug-resistant organisms (MDROs) is one of the most urgent public health threats affecting both humans and animals. The One Health concept emphasizes the interconnectedness of human, animal and environmental health and highlights the need for integrated approaches to combat antimicrobial resistance (AMR). Although the sharing of environments and antimicrobial agents between companion animals and humans poses a risk for MDRO transmission, companion animals have been studied to a lesser extent than livestock animals. This study therefore used core genome multilocus sequence typing (cgMLST) to investigate the genetic relationships and putative transmission of MDROs between humans and pets. Methods: This descriptive integrated typing study included 252 human isolates, 53 dog isolates and 10 cat isolates collected from 2019 to 2022 at the Charité University Hospital in Berlin, Germany. CgMLST was performed to characterize methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci and multidrug-resistant gram-negative bacteria. The genetic diversity of the MDROs of the different host populations was determined and compared based on sequence type and core genome complex type. Results: Within this study the majority of samples from pets and humans was genetically distinct. However, for some isolates, the number of allelic differences identified by cgMLST was low. Two cases of putative household transmission or shared source of VR E. faecium and MDR E. coli between humans and pets were documented. Conclusions: The interaction between humans and their pets appears to play a minor role in the spread of the MDROs studied. However, further research is needed. This study emphasizes the importance of comprehensive molecular surveillance and a multidisciplinary One Health approach to understand and contain the spread of MDROs in human and animal populations. Trial Registration: The study is registered with the German Clinical Trials Register (DRKS00030009). [ABSTRACT FROM AUTHOR]

The tannery industry produces one of the worst contaminants, and unsafe disposal in nearby waterbodies and landfills has become an imminent threat to public health, especially when the resulting multidrug-resistant bacteria and heavy metals enter community settings and animal food chains. In this study, we have collected 10 tannery wastewater (TWW) samples and 10 additional non-tannery wastewater (NTW) samples to compare the chemical oxygen demand (COD), pH, biological oxygen demand (BOD), dissolved oxygen (DO), total dissolved solids (TDS), chromium concentration, bacterial load, and antibiotic resistance profiles. While COD, pH, and chromium concentration data were previously published from our lab, this part of the study uncovers that TWW samples had a significantly higher bacterial load, compared to the non-tannery wastewater samples (5.89 × 104 and 9.38 × 103 cfu/mL, respectively), higher BOD and TDS values, and significantly lower DO values. The results showed that 53.4, 46.7, 40.0, and 40.0% of the TWW isolates were resistant to ceftriaxone, erythromycin, nalidixic acid, and azithromycin, respectively. On the other hand, 20.0, 30.0, 50.0, and 40.0% of the NTW isolates were resistant to the same antibiotics, respectively. These findings suggest that the TWW isolates were more resistant to antibiotics than the NTW isolates. Moreover, the TWW isolates exhibited higher multidrug resistance than the NTW isolates, 33.33, and 20.00%, respectively. Furthermore, spearman correlation analysis depicts that there is a negative correlation between BOD and bacterial load up to a certain level (r = − 0.7749, p = 0.0085). In addition, there is also a consistent negative correlation between COD and bacterial load (r = − 0.7112, p = 0.0252) and TDS and bacterial load (r = − 0.7621, p = 0.0104). These findings suggest that TWW could pose a significant risk to public health and the environment and highlight the importance of proper wastewater treatment in tannery industries. [ABSTRACT FROM AUTHOR]

Intra-abdominal infections (IAIs) are one of the important contributors to sepsis in intensive care units. The emergence of antibiotic resistance and the diversification of etiological agents make it challenging to determine the optimal empirical therapy. This study attempts to know the etiological agents, their antibiotic susceptibility patterns, and the risk factors associated with IAIs in different settings. This prospective cross-sectional study was conducted in a tertiary care facility from January 2023 to June 2023. Adult and paediatric patients having primary IAI or developed infections during their hospital stay were included in this study. Specimen like peritoneal swabs or fluid from intra-abdominal drains placed for more than 24 hours were excluded. Matrix-assisted Laser Desorption/Ionization Time-Of-Flight was used to identify the etiological agents. VITEK®2 system was used to perform the antimicrobial susceptibility. Associated risk factors were documented. A total of 86 cases were analysed. The majority of the patients had complicated IAIs (95.3%), and 65.12 % acquired the infection in the community (CAIAI). The vast number of cases presented with intra-abdominal abscesses (46.5%). Diabetes and hepatic disorders were the frequent underlying comorbid conditions associated with CA-IAIs. Prolonged hospital stay and the presence of concomitant conditions like malignancy and chronic renal failure significantly influenced the occurrence of hospital-acquired infections (HA-IAIs). E. coli was the frequently isolated Gram-negative pathogen both in the community and hospital settings. Whereas among Gram-positives, Enterococcus predominated and was commonly isolated from HA-IAIs. Enterobacterales were highly susceptible to meropenem and piperacillin-tazobactam. E. coli and Klebsiella were the frequent extendedspectrum beta-lactamase producers and showed the least susceptibility towards cephalosporins and fluoroquinolones. Multidrug-resistant organisms (MDROs) (p=.013), including carbapenem-resistant strains (p=.048), were significantly isolated from hospital-acquired IAIs. The high prevalence of IAIs with MDROs in hospital settings emphasizes the importance of developing hospital-based antibiotic policy, infection control measures, and judicious use of antibiotics. [ABSTRACT FROM AUTHOR]

Endolysin, a bacteriophage-derived lytic enzyme, has emerged as a promising alternative antimicrobial agent against rising multidrug-resistant bacterial infections. Two novel endolysins LysPEF1-1 and LysPEF1-2 derived from Enterococcus phage PEF1 were cloned and overexpressed in Escherichia coli to test their antimicrobial efficacy against multidrug-resistant E. faecalis strains and their biofilms. LysPEF1-1 comprises an enzymatically active domain and a cell-wall-binding domain originating from the NLPC-P60 and SH3 superfamilies, while LysPEF1-2 contains a putative peptidoglycan recognition domain that belongs to the PGRP superfamily. LysPEF1-1 was active against 89.86% (62/69) of Enterococcus spp. tested, displaying a wider antibacterial spectrum than phage PEF1. Moreover, two endolysins demonstrated lytic activity against additional gram-positive and gram-negative species pretreated with chloroform. LysPEF1-1 showed higher activity against multidrug-resistant E. faecalis strain E5 than LysPEF1-2. The combination of two endolysins effectively reduced planktonic cells of E5 in broth and was more efficient at inhibiting biofilm formation and removing biofilm cells of E. faecalis JCM 7783T than used individually. Especially at 4 °C, they reduced viable biofilm cells by 4.5 log after 2 h of treatment on glass slide surfaces. The results suggest that two novel endolysins could be alternative antimicrobial agents for controlling E. faecalis infections. [ABSTRACT FROM AUTHOR]

Background: Wound infections have been a problem in the field of medicine for a long time due to the emergence and re-emergence of drug resistance. The assessment of Betalactamase production, plasmid profiling and corresponding resistance pattern in the local terrain become important for a proper understanding of wound infection burden and its epidemiology. The study aimed to assess beta-lactamase production among multidrugresistant wound isolates from patients attending University College Hospital (UCH), Ibadan. Methods: Sample size of 370 was determined using the Cochran formula. Exudates from wounds were collected with sterile swab sticks, isolation and identification were performed using standard procedures. Antimicrobial susceptibility testing was carried out using the Kirby-Bauer disc diffusion method, Beta Lactamase Production was carried out using the starch iodide acidimetric method. Double disc synergy test and combination disk were used for extended–spectrum beta-lactamases (ESBL) and metallo-beta-lactamase (MBL) detection respectively. Plasmid curing of two beta-lactamase procedures was carried out using sodium dodecyl sulphate (SDS). After which, post-curing antibiotics susceptibility testing was performed. Results: Result shows 339 isolates of which 56.9% were multidrugresistant. Beta-lactamase producers were 60.7% from which 5% and 14% were positive for ESBL and MBL test. Same resistance pattern to the antibiotics was observed in plasmidcured isolates, meaning that their resistance was not plasmid-mediated. Conclusion: The establishment of beta-lactamase producing capacity in the wound isolates in this study will help clinicians in the appropriate treatment of wound infections. [ABSTRACT FROM AUTHOR]

Given the lack of genetic characterization data for multidrug-resistant (MDR) Salmonella in South Korean poultry, we analyzed 53 MDR Salmonella strains from 1232 poultry meat samples (723 chicken, 509 duck) using whole-genome sequencing. Five serotypes were identified: S. Infantis (30/53, 56.6%), S. Enteritidis (11/53, 20.8%), S. Virchow (9/53, 17.0%), S. Agona (2/53, 3.8%), and S. Indiana (1/53, 1.9%). Sequence types (STs) included ST32, ST11, ST16, ST13, and ST17, with three major clusters, each having two subclusters. Eight core genome sequence types (cgSTs) were identified: 225993, 2268, 58360, 150996, 232041, 96964, 117577, and 267045. Salmonella Infantis and S. Enteritidis had two (117577, 267045) and three (225993, 2268, 58360) cgSTs, respectively, whereas S. Virchow showed allelic differences in identical cgSTs. The S. Enteritidis subcluster was classified as chicken or duck. Twenty-eight antimicrobial resistance genes (ARGs), 10 plasmid replicons, 11 Salmonella pathogenicity islands (SPIs), and 230 virulence genes were identified, showing distinct profiles by cluster and subcluster. Salmonella Infantis, the primary MDR Salmonella, carried the IncFIB (pN55391) plasmid, 10–11 ARGs, nine SPIs, and approximately 163 virulence genes. Three major MDR Salmonella serotypes (S. Infantis, S. Enteritidis, and S. Virchow) had specific genetic profiles that can inform epidemiological surveillance. [ABSTRACT FROM AUTHOR]

Intra-abdominal infections (IAIs) are one of the important contributors to sepsis in intensive care units. The emergence of antibiotic resistance and the diversification of etiological agents make it challenging to determine the optimal empirical therapy. This study attempts to know the etiological agents, their antibiotic susceptibility patterns, and the risk factors associated with IAIs in different settings. This prospective cross-sectional study was conducted in a tertiary care facility from January 2023 to June 2023. Adult and paediatric patients having primary IAI or developed infections during their hospital stay were included in this study. Specimen like peritoneal swabs or fluid from intra-abdominal drains placed for more than 24 hours were excluded. Matrix-assisted Laser Desorption/Ionization Time-Of-Flight was used to identify the etiological agents. Vitek®2 system was used to perform the antimicrobial susceptibility. Associated risk factors were documented. A total of 86 cases were analysed. The majority of the patients had complicated IAIs (95.3%), and 65.12 % acquired the infection in the community (CA-IAI). The vast number of cases presented with intra-abdominal abscesses (46.5%). Diabetes and hepatic disorders were the frequent underlying comorbid conditions associated with CA-IAIs. Prolonged hospital stay and the presence of concomitant conditions like malignancy and chronic renal failure significantly influenced the occurrence of hospital-acquired infections (HA-IAIs). E. coli was the frequently isolated Gram-negative pathogen both in the community and hospital settings. Whereas among Gram-positives, Enterococcus predominated and was commonly isolated from HA-IAIs. Enterobacterales were highly susceptible to meropenem and piperacillin-tazobactam. E. coli and Klebsiella were the frequent extended-spectrum beta-lactamase producers and showed the least susceptibility towards cephalosporins and fluoroquinolones. Multidrug-resistant organisms (MDROs) (p=.013), including carbapenem-resistant strains (p=.048), were significantly isolated from hospital-acquired IAIs. The high prevalence of IAIs with MDROs in hospital settings emphasizes the importance of developing hospital-based antibiotic policy, infection control measures, and judicious use of antibiotics.

Yuanzhong Fang,1 Juan Jin,1 Minfei Peng,2 Lidong Xu,1 Linyuan Gu,1 Danni Bao,3 Qiuying Zhang,4 Kainan Jin5 1Department of Clinical Laboratory, Hangzhou Linping District Women & Children Hospital, Hangzhou, Zhejiang, People’s Republic of China; 2Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, 317000, People’s Republic of China; 3Department of Clinical Laboratory, Sanmen People’s Hospital, Sanmen Bay Branch of The First Affiliated Hospital, Zhejiang University School of Medicine, Taizhou, Zhejiang, 317100, People’s Republic of China; 4Department of Clinical Laboratory, Suizhou Hospital, Hubei University of Medicine, Suizhou, Hubei, People’s Republic of China; 5Department of Gastroenterology, Linhai First People’s Hospital, Taizhou, Zhejiang, 317000, People’s Republic of ChinaCorrespondence: Qiuying Zhang, Department of Clinical Laboratory, Suizhou Hospital, Hubei University of Medicine, Suizhou, Hubei, People’s Republic of China, Email 26067889@qq.com Kainan Jin, Department of Gastroenterology, Linhai first People’s hospital, Taizhou, Zhejiang, 317000, People’s Republic of China, Email 353803262@qq.comBackground: Hypervirulent carbapenem-resistant K. pneumoniae (hv-CRKP) has been spreading rapidly worldwide. Here, we investigated the genomic characteristics of ST11 K. pneumoniae isolate SM117 with capsular serotype KL25, co-carrying blaNDM-5, two copies of blaKPC-2 and multiple plasmid-borne virulence genes from a county level hospital in China.Methods: Antimicrobial susceptibility of K. pneumoniae SM117 was evaluated. The Illumina NovaSeq 6000 and Oxford Nanopore MinION platforms were applied to sequence the genome and then de novo assembled. The genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline and further subjected to identify the sequence type (ST), capsular type, antibiotic resistance genes, plasmid replicon types and virulence genes. The phylogenetic analysis was performed based on the core genome single nucleotide polymorphisms (cgSNPs) using CSI Phylogeny 1.4, and further visualized by Interactive Tree of Life (iTOL) V5 web server.Results: The whole-genome sequence of K. pneumoniae SM117 is made up of eight contigs totaling 6,104,486 bp, contain a 5,612,620 bp single chromosome and seven plasmids. The isolate was assigned to ST11 with capsular serotype KL25, co-carrying including blaNDM-5, blaKPC-2 and multiple plasmid-borne virulence genes including rmpA2 and aerobactin genes iucABCD-iutA. The coexistence of blaKPC and blaNDM in K. pneumoniae strains exhibit a high degree of resistance to β-lactam antibiotics. The strain SM117 also carries multiple antibiotic resistance genes, making it resistant to all antibiotics except polymyxin. The closest relative of K. pneumoniae C793 was identified in 2023 from a hospital surface sample in Zhejiang, China, with just 52 SNPs difference.Conclusion: This study reported the genomic characteristics of a multidrug-resistant ST11 K. pneumoniae with capsular serotype KL25, co-carrying blaNDM-5, two copies of blaKPC-2 genes and multiple plasmid-borne virulence genes in China. These findings will provide important knowledge of the antibiotic resistance mechanisms, genomic epidemiological characteristics and transmission dynamics of multidrug-resistant K. pneumoniae.Keywords: whole-genome sequencing, K. pneumoniae, multidrug-resistance, blaNDM-5, blaKPC-2, rmpA2, iucABCD-iutA, hvCRKP

Abstract The tannery industry produces one of the worst contaminants, and unsafe disposal in nearby waterbodies and landfills has become an imminent threat to public health, especially when the resulting multidrug-resistant bacteria and heavy metals enter community settings and animal food chains. In this study, we have collected 10 tannery wastewater (TWW) samples and 10 additional non-tannery wastewater (NTW) samples to compare the chemical oxygen demand (COD), pH, biological oxygen demand (BOD), dissolved oxygen (DO), total dissolved solids (TDS), chromium concentration, bacterial load, and antibiotic resistance profiles. While COD, pH, and chromium concentration data were previously published from our lab, this part of the study uncovers that TWW samples had a significantly higher bacterial load, compared to the non-tannery wastewater samples (5.89 × 104 and 9.38 × 103 cfu/mL, respectively), higher BOD and TDS values, and significantly lower DO values. The results showed that 53.4, 46.7, 40.0, and 40.0% of the TWW isolates were resistant to ceftriaxone, erythromycin, nalidixic acid, and azithromycin, respectively. On the other hand, 20.0, 30.0, 50.0, and 40.0% of the NTW isolates were resistant to the same antibiotics, respectively. These findings suggest that the TWW isolates were more resistant to antibiotics than the NTW isolates. Moreover, the TWW isolates exhibited higher multidrug resistance than the NTW isolates, 33.33, and 20.00%, respectively. Furthermore, spearman correlation analysis depicts that there is a negative correlation between BOD and bacterial load up to a certain level (r = − 0.7749, p = 0.0085). In addition, there is also a consistent negative correlation between COD and bacterial load (r = − 0.7112, p = 0.0252) and TDS and bacterial load (r = − 0.7621, p = 0.0104). These findings suggest that TWW could pose a significant risk to public health and the environment and highlight the importance of proper wastewater treatment in tannery industries.

Objective: In Ecuador, data on molecular epidemiology, as well as circulating clones, are limited. Therefore, this study aims to know the population structure of Pseudomonas aeruginosa by identifying clones in clinical samples in Quito-Ecuador. Methods: A significant set (45) clinical P. aeruginosa isolates were selected, including multidrug and non-multidrug resistant isolates, which were assigned to sequence types (STs) and compared with their antibiotic susceptibility profile. The genetic diversity was assessed by applying the multilocus sequence typing (MLST) scheme and the genetic relationships between different STs were corroborated by phylogenetic networks. Results: The MLST analysis identified 24 different STs and the most prevalent STs were ST-3750 and ST-253. The majority of the multidrug-resistance (MDR) isolates were included in ST-3750 and ST-253, also 3 singleton STs were identified as MDR isolates. The 21 different STs were found in non-multidrug resistance (non-MDR) isolates, and only 3 STs were found in more the one isolate. Conclusions: The population structure of clinical P. aeruginosa present in these isolates indicates a significant association between MDR isolates and the clonal types: all ST-3750 and ST-253 isolates were MDR. ST-3750 is a closely related strain to the clonal complex ST111 (CC111). ST-253 and ST111 are a group of successful high-risk clones widely distributed worldwide. The multiresistant isolates studied are grouped in the most prevalent STs found, and the susceptible isolates correspond mainly with singleton STs. Therefore, these high-risk clones and their association with MDR phenotypes are contributing to the spread of MDR in Quito, Ecuador.

The prevalence of carbapenem-resistant P. aeruginosa has dramatically increased over the last decade, and antibiotics alone are not enough to eradicate infections caused by this opportunistic pathogen. Phage therapy is a fresh treatment that can be administered under compassionate use, particularly against chronic cases. However, it is necessary to thoroughly characterize the virus before therapeutic application. Our work describes the discovery of the novel sequenced bacteriophage, vB_PaeP-F1Pa, containing an integrase, performs a phylogenetical analysis, describes its stability at a physiological pH and temperature, latent period (40 min), and burst size (394 ± 166 particles per bacterial cell), and demonstrates its ability to infect MDR and XDR P. aeruginosa strains. Moreover, this novel bacteriophage was able to inhibit the growth of bacteria inside preformed biofilms. The present study offers a road map to analyze essential areas for successful phage therapy against MDR and XDR P. aeruginosa infections, and shows that a phage containing an integrase is also able to show good in vitro results, indicating that it is very important to perform a genomic analysis before any clinical use, in order to prevent adverse effects in patients. [ABSTRACT FROM AUTHOR]

Introduction: The surge of multidrug-resistant TB (MDR-TB) in Iran poses a significant challenge to global healthcare. The introduction of delamanid (DLM) and bedaquiline (BDQ), two potent antimycobacterial drugs, marks a crucial advance. Nevertheless, as resistance in Mycobacterium tuberculosis is on the rise in Iran and resistance to these newer medications is emerging, investigations in this field are of utmost importance. Methods: In this cross-sectional study, 38 MDR-TB strains were collected from five distinct regional TB laboratories in Iran. The clinical isolates were confirmed as M. tuberculosis using the phenotypic tests and IS6110-based PCR assay. Drug susceptibility testing (DST) for isoniazid, rifampicin, ethambutol, DLM, and BDQ was performed using WHO-approved methods. Sequencing was used to investigate genetic mutations in DLM (ddn, fgd1) and BDQ (Rv0678, atpE, pepQ) genes associated with resistance. Results: Among the 38 collected MDR-TB isolates, 7 (18.5 %) exhibited resistance to DLM, while all remained susceptible to BDQ. Analysis of the sequencing data revealed that the ddn gene exhibited the highest number of mutations in DLM-resistant isolates, including 18 nonsynonymous mutations and 1 indel leading to frameshift mutations. A common mutation, Gly81Ser, was present in 4 of the DLM-resistant isolates (4/7; 57.1 %). A synonymous mutation, T960C, in the fgd1 gene was uniformly found in DLM-resistant samples. Notably, no significant mutations were observed in the atpE, Rv0678, or pepQ genes in any of the BDQ-susceptible isolates. Conclusions: Our study underscores the emergence of DLM resistance in a subset of MDR-TB isolates in Iran, primarily associated with mutations in the ddn gene. This emphasizes the ongoing necessity for TB drug resistance surveillance and research. While BDQ remains efficacious, the emergence of DLM resistance is a concerning development, warranting further exploration into resistance mechanisms and the formulation of effective TB control strategies.

Background: The accelerating prevalence of extended-spectrum β-lactamase (ESBL)-producing and multidrug-resistance (MDR) Escherichia coli (E. coli) become a public health challenge worldwide. This study aimed to discuss the prevalence of drug-resistant E. coli colonization and analyze its risk factors and clinical characteristics among young infants in Southern Taiwan. Methods: Stool samples were collected from young infants, aged less than three months, within three days of their hospitalization from September to December 2019 in a tertiary hospital. A questionnaire was designed for parents to complete. E. coli colonies were selected and analyzed for antimicrobial susceptibility. PCR-based multilocus sequence typing was to detect the presence of sequence type ST131 and blaCTX-M genes. Results: Among 100 enrolled infants, 36% had fecal carriage of E. coli isolates, of which twenty nine (80.5%) were MDR, thirteen (36.1%) were ESBL-producing isolates and five (13.8%) and ten (27.7%) were ST131 and strains carrying CTX-M-14 gene, respectively. Compared to non-ST131 and non-CTX-M-14 gene carrier, isolates of ST131 and CTX-M-14 gene carrier showed a significantly higher resistance rate to cefixime, ceftriaxone, and gentamycin, with p value all

Objective: Food-borne illnesses pose a significant risk to public health on a global scale and are a major contributing factor to illness and death rates worldwide. Salmonella strains found in chicken meat and its related products may be the likely source of a multi-country outbreak. Research is scarce regarding the occurrence of antimicrobial-resistant Salmonella in chicken meat within Afghanistan; therefore, in the present study, the aim was to identify Salmonella found in uncooked chicken meat in the local markets of Kabul city and ascertain their susceptibility to commonly used antibiotics. Materials and Methods: One hundred raw chicken meats were gathered from four districts of Kabul city from May 2022 until April 2023; the isolates were then identified using culture, biochemical tests, and the analytical profile index; an examination of antimicrobial susceptibility was conducted utilizing the disk diffusion technique. Results: Out of 100 samples, only 8 (8%) tested positive for Salmonella spp. The disk diffusion results from Salmonella-positive samples showed multidrug resistance; maximum resistance was against ampicillin (100%) followed by norfloxacin (75%), nalidixic acid (62.5%), cefoxitin (62.5%), tetracycline, and ciprofloxacin (50%). Conclusion: The global occurrence of foodborne infections and antibiotic resistance has increased and preserved public health concerns around the world. Identifying zoonotic bacteria and their antimicrobial resistance patterns is critical for controlling their transmission and facilitating effective antimicrobial therapy in both humans and animals. [Vet. Res. Notes 2024; 4(3.000): 24-29]

The accelerating prevalence of extended-spectrum β-lactamase (ESBL)-producing and multidrug-resistance (MDR) Escherichia coli (E. coli) become a public health challenge worldwide. This study aimed to discuss the prevalence of drug-resistant E. coli colonization and analyze its risk factors and clinical characteristics among young infants in Southern Taiwan. Stool samples were collected from young infants, aged less than three months, within three days of their hospitalization from September to December 2019 in a tertiary hospital. A questionnaire was designed for parents to complete. E. coli colonies were selected and analyzed for antimicrobial susceptibility. PCR-based multilocus sequence typing was to detect the presence of sequence type ST131 and bla CTX-M genes. Among 100 enrolled infants, 36% had fecal carriage of E. coli isolates, of which twenty nine (80.5%) were MDR, thirteen (36.1%) were ESBL-producing isolates and five (13.8%) and ten (27.7%) were ST131 and strains carrying CTX-M-14 gene, respectively. Compared to non-ST131 and non-CTX-M-14 gene carrier, isolates of ST131 and CTX-M-14 gene carrier showed a significantly higher resistance rate to cefixime, ceftriaxone, and gentamycin, with p value all <0.05. The prevalence of ESBL-producing and MDR E. coli fecal carriage were both high in young infants. The most common sequence type is ST131, of which all are strains carrying CTX-M-14. Further surveillance and investigation to control for the high prevalence of antimicrobial-resistant E. coli fecal carriage among infants in Taiwan are warranted. [ABSTRACT FROM AUTHOR]

Antimicrobial-resistant bacteria are frequently isolated from retail meat and may infect humans. To determine the diversity of antimicrobial-resistant bacteria in Australian retail meat, bacteria were cultured on selective media from raw chicken (n = 244) and pork (n = 160) meat samples obtained from all four major supermarket chains in the ACT/NSW, Australia, between March and June 2021. Antimicrobial susceptibility testing (AST) was performed for 13 critically and 4 highly important antibiotics as categorised by the World Health Organization (WHO) for a wide range of species detected in the meat samples. A total of 288 isolates underwent whole-genome sequencing (WGS) to identify the presence of antimicrobial resistance (AMR) genes, virulence genes, and plasmids. AST testing revealed that 35/288 (12%) of the isolates were found to be multidrug-resistant (MDR). Using WGS data, 232/288 (81%) of the isolates were found to harbour resistance genes for critically or highly important antibiotics. This study reveals a greater diversity of AMR genes in bacteria isolated from retail meat in Australia than previous studies have shown, emphasising the importance of monitoring AMR in not only foodborne pathogenic bacteria, but other species that are capable of transferring AMR genes to pathogenic bacteria. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance is a critical challenge due to the overuse of conventional antimicrobials, and alternative solutions are urgently needed. This study investigates the efficacy of compounds derived from lactic acid bacteria (LAB) fermentation combined with antibiotics against multidrug-resistant pathogens isolated from clinical cases in a hospital setting. Strains of Escherichia coli, Klebsiella pneumoniae, and Enterococcus faecium and faecalis were isolated and selected from blood, respiratory, and urine samples. They were tested against the fermentation products from the Ingulados LAB collection (BAL5, BAL6, BAL8, BAL13, and BAL16), recognized for their antimicrobial efficacy against veterinary pathogens. The activity against multidrug-resistant (MDR) pathogens was evaluated initially, followed by synergy tests using checkerboard assays and subsequent analysis. Bioinformatic assessments and supernatant treatments were performed to characterize the nature of the compounds responsible for the antimicrobial activity. Notably, BAL16 exhibited significant growth inhibition against multidrug-resistant E. faecium. Synergy tests highlighted its combined activity with tetracycline through FICI and surface analysis and bioinformatic analysis unveiled the protein fraction containing bacteriocins as the underlying mechanism. This study highlights BAL16 fermentation products potential as valuable antimicrobial agents against MDR E. faecium infections, attributed to bacteriocins. Further in-depth studies are necessary for complete bacteriocin characterization. [ABSTRACT FROM AUTHOR]

Background and Aim: Farm animals, including cattle, have been implicated as antimicrobial-resistant bacterial pathogen reservoirs. This study aimed to determine the antimicrobial resistance profiles and genetic characteristics of cattle colonized by fluoroquinolone-resistant and extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in Ebonyi state, Nigeria. Materials and Methods: We randomly collected 100 fresh fecal samples from 100 cattle in major abattoirs and analyzed the samples using standard microbiological methods. Isolates were further characterized by polymerase chain reaction (PCR) using 16S rRNA sequence primers. Phenotypic detection of ESBL production was performed using the double disk synergy test. Antimicrobial susceptibility profiles of ESBL-producing Escherichia coli were determined using the disk diffusion method, whereas molecular characterization of ESBL- and fluoroquinolone-resistant genes was performed by PCR using specific primers. Results: A total of 20 (20%) ESBL-producing E. coli were isolated from 100 animal fecal samples. Isolates were generally multidrug-resistant (MDR) with a resistance rate of 100% to 45% to trimethoprim-sulfamethoxazole, tetracycline, amoxicillin, cephalosporins, and ciprofloxacin. The average multiple antibiotic resistance index values of the isolates ranged from 0.5 to 0.8. BlaTEM (75%), followed by blaCTX-M (20%) and blaSHV (5.0%) was the most predominant ESBL gene among the isolates. The Aac-lb-6-cr fluoroquinolone-resistant gene was harbored by 90% of the isolates, whereas Qnr was absent. Conclusion: This study showed a high frequency of MDR ESBL-producing E. coli harboring ESBL and fluoroquinolone-resistant genes in fecal samples of cattle with serious public health consequences if not adequately addressed.

Abstract Background Extended-spectrum β-lactamase (ESBL), plasmid-mediated AmpC-β-lactamase and carbapenemase-producing Escherichia coli and Klebsiella pneumoniae have spread into the environment worldwide posing a potential public health threat. However, the prevalence data for low- and middle-income countries are still scarce. The aim of this study was to evaluate the presence of ESBL, AmpC-β-lactamase and carbapenemase-producing and multidrug-resistant E. coli and K. pneumoniae in wastewaters from healthcare centers in Burkina Faso. Results Eighty-four (84) wastewater samples were collected from five healthcare centers and plated on selective ESBL ChromAgar. E. coli and Klebsiella pneumoniae isolates were identified using API20E. ESBL-producing bacteria were detected in 97.6% of the samples and their average concentration per hospital ranged from 1.10 × 105 to 5.23 × 106 CFU/mL. Out of 170 putative ESBL-producing isolates (64% of them were E. coli) and 51 putative AmpC-β-lactamase-producing isolates, 95% and 45% were confirmed, respectively. Carbapenemase production was detected in 10 isolates, of which 6 were NDM producers, 3 were OXA-48 producers and 1 was NDM and OXA-48 producer. All isolates were multidrug resistant and, moreover, all of them were resistant to all tested β-lactams. Resistance to ESBL inhibitors was also common, up to 66% in E. coli and 62% in K. pneumoniae. Amikacin, fosfomycin and nitrofurantoin were the antibiotics to which the least resistance was detected. Conclusions This study showed that wastewater from healthcare centers constitutes a reservoir of multidrug-resistant bacteria in Burkina Faso, including carbapenemase producers. Untreated healthcare wastewater entering the environment exposes people and animals to infections caused by these multi-resistant bacteria, which are difficult to treat, especially in the resource-poor settings.

Endolysin, a bacteriophage-derived lytic enzyme, has emerged as a promising alternative antimicrobial agent against rising multidrug-resistant bacterial infections. Two novel endolysins LysPEF1-1 and LysPEF1-2 derived from Enterococcus phage PEF1 were cloned and overexpressed in Escherichia coli to test their antimicrobial efficacy against multidrug-resistant E. faecalis strains and their biofilms. LysPEF1-1 comprises an enzymatically active domain and a cell-wall-binding domain originating from the NLPC-P60 and SH3 superfamilies, while LysPEF1-2 contains a putative peptidoglycan recognition domain that belongs to the PGRP superfamily. LysPEF1-1 was active against 89.86% (62/69) of Enterococcus spp. tested, displaying a wider antibacterial spectrum than phage PEF1. Moreover, two endolysins demonstrated lytic activity against additional gram-positive and gram-negative species pretreated with chloroform. LysPEF1-1 showed higher activity against multidrug-resistant E. faecalis strain E5 than LysPEF1-2. The combination of two endolysins effectively reduced planktonic cells of E5 in broth and was more efficient at inhibiting biofilm formation and removing biofilm cells of E. faecalis JCM 7783T than used individually. Especially at 4 °C, they reduced viable biofilm cells by 4.5 log after 2 h of treatment on glass slide surfaces. The results suggest that two novel endolysins could be alternative antimicrobial agents for controlling E. faecalis infections.

Given the lack of genetic characterization data for multidrug-resistant (MDR) Salmonella in South Korean poultry, we analyzed 53 MDR Salmonella strains from 1232 poultry meat samples (723 chicken, 509 duck) using whole-genome sequencing. Five serotypes were identified: S. Infantis (30/53, 56.6%), S. Enteritidis (11/53, 20.8%), S. Virchow (9/53, 17.0%), S. Agona (2/53, 3.8%), and S. Indiana (1/53, 1.9%). Sequence types (STs) included ST32, ST11, ST16, ST13, and ST17, with three major clusters, each having two subclusters. Eight core genome sequence types (cgSTs) were identified: 225993, 2268, 58360, 150996, 232041, 96964, 117577, and 267045. Salmonella Infantis and S. Enteritidis had two (117577, 267045) and three (225993, 2268, 58360) cgSTs, respectively, whereas S. Virchow showed allelic differences in identical cgSTs. The S. Enteritidis subcluster was classified as chicken or duck. Twenty-eight antimicrobial resistance genes (ARGs), 10 plasmid replicons, 11 Salmonella pathogenicity islands (SPIs), and 230 virulence genes were identified, showing distinct profiles by cluster and subcluster. Salmonella Infantis, the primary MDR Salmonella, carried the IncFIB (pN55391) plasmid, 10–11 ARGs, nine SPIs, and approximately 163 virulence genes. Three major MDR Salmonella serotypes (S. Infantis, S. Enteritidis, and S. Virchow) had specific genetic profiles that can inform epidemiological surveillance.

Background and Aim: Farm animals, including cattle, have been implicated as antimicrobial-resistant bacterial pathogen reservoirs. This study aimed to determine the antimicrobial resistance profiles and genetic characteristics of cattle colonized by fluoroquinolone-resistant and extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in Ebonyi state, Nigeria. Materials and Methods: We randomly collected 100 fresh fecal samples from 100 cattle in major abattoirs and analyzed the samples using standard microbiological methods. Isolates were further characterized by polymerase chain reaction (PCR) using 16S rRNA sequence primers. Phenotypic detection of ESBL production was performed using the double disk synergy test. Antimicrobial susceptibility profiles of ESBL-producing Escherichia coli were determined using the disk diffusion method, whereas molecular characterization of ESBL- and fluoroquinolone-resistant genes was performed by PCR using specific primers. Results: A total of 20 (20%) ESBL-producing E. coli were isolated from 100 animal fecal samples. Isolates were generally multidrug-resistant (MDR) with a resistance rate of 100% to 45% to trimethoprim-sulfamethoxazole, tetracycline, amoxicillin, cephalosporins, and ciprofloxacin. The average multiple antibiotic resistance index values of the isolates ranged from 0.5 to 0.8. BlaTEM (75%), followed by blaCTX-M (20%) and blaSHV (5.0%) was the most predominant ESBL gene among the isolates. The Aac-lb-6-cr fluoroquinolone-resistant gene was harbored by 90% of the isolates, whereas Qnr was absent. Conclusion: This study showed a high frequency of MDR ESBL-producing E. coli harboring ESBL and fluoroquinoloneresistant genes in fecal samples of cattle with serious public health consequences if not adequately addressed. [ABSTRACT FROM AUTHOR]

The Beijing genotype is the most distributed M. tuberculosis family in Kazakhstan. In this study, we identified dominant Beijing clusters in Kazakhstan and assessed their drug susceptibility profiles and association with the most widely spread mutation Ser531Leu of the rpoB gene and the mutation Ser315Thr of the katG gene associated with resistance to rifampicin and isoniazid, respectively. M. tuberculosis isolates (n = 540) from new TB cases were included in the study. MIRU-VNTR genotyping was performed for 540 clinical isolates to determine M. tuberculosis families using 24 loci. RD analysis was additionally performed for the Beijing isolates. The identification of mutations in the drug-resistance genes of M. tuberculosis was performed with allele-specific real-time PCR and Sanger sequencing. The Beijing genotype was identified in 60% (324/540) of the clinical isolates. Central Asian/Russian cluster 94-32 was the most distributed cluster among the Beijing isolates (50.3%; 163/324). Three other dominant Beijing clusters were identified as 94-33 (3.4%; 11/324), 100-32 (3.1%; 10/324) and 99-32 (3.1%; 10/324). The Beijing genotype was associated with drug-resistant TB (p < 0.0001), including multidrug-resistant TB (p < 0.0001), in our study. An association of the mutation Ser531Leu of the rpoB gene with the Beijing genotype was found (p < 0.0001; OR = 16.0000; 95%CI: 4.9161–52.0740). Among the Beijing isolates, cluster 94-32 showed an association with MDR-TB (p = 0.021). This is why the evaluation of the Beijing genotype and its clusters is needed to control MDR-TB in Kazakhstan. [ABSTRACT FROM AUTHOR]

Background: Extended-spectrum β-lactamase (ESBL), plasmid-mediated AmpC-β-lactamase and carbapenemase-producing Escherichia coli and Klebsiella pneumoniae have spread into the environment worldwide posing a potential public health threat. However, the prevalence data for low- and middle-income countries are still scarce. The aim of this study was to evaluate the presence of ESBL, AmpC-β-lactamase and carbapenemase-producing and multidrug-resistant E. coli and K. pneumoniae in wastewaters from healthcare centers in Burkina Faso. Results: Eighty-four (84) wastewater samples were collected from five healthcare centers and plated on selective ESBL ChromAgar. E. coli and Klebsiella pneumoniae isolates were identified using API20E. ESBL-producing bacteria were detected in 97.6% of the samples and their average concentration per hospital ranged from 1.10 × 105 to 5.23 × 106 CFU/mL. Out of 170 putative ESBL-producing isolates (64% of them were E. coli) and 51 putative AmpC-β-lactamase-producing isolates, 95% and 45% were confirmed, respectively. Carbapenemase production was detected in 10 isolates, of which 6 were NDM producers, 3 were OXA-48 producers and 1 was NDM and OXA-48 producer. All isolates were multidrug resistant and, moreover, all of them were resistant to all tested β-lactams. Resistance to ESBL inhibitors was also common, up to 66% in E. coli and 62% in K. pneumoniae. Amikacin, fosfomycin and nitrofurantoin were the antibiotics to which the least resistance was detected. Conclusions: This study showed that wastewater from healthcare centers constitutes a reservoir of multidrug-resistant bacteria in Burkina Faso, including carbapenemase producers. Untreated healthcare wastewater entering the environment exposes people and animals to infections caused by these multi-resistant bacteria, which are difficult to treat, especially in the resource-poor settings. [ABSTRACT FROM AUTHOR]

Summary: Background: The current pipeline for new antibiotics fails to fully address the significant threat posed by drug-resistant Gram-negative bacteria that have been identified by the World Health Organization (WHO) as a global health priority. New antibacterials acting through novel mechanisms of action are urgently needed. We aimed to identify new chemical entities (NCEs) with activity against Klebsiella pneumoniae and Acinetobacter baumannii that could be developed into a new treatment for drug-resistant infections. Methods: We developed a high-throughput phenotypic screen and selection cascade for generation of hit compounds active against multidrug-resistant (MDR) strains of K. pneumoniae and A. baumannii. We screened compound libraries selected from the proprietary collections of three pharmaceutical companies that had exited antibacterial drug discovery but continued to accumulate new compounds to their collection. Compounds from two out of three libraries were selected using “eNTRy rules” criteria associated with increased likelihood of intracellular accumulation in Escherichia coli. Findings: We identified 72 compounds with confirmed activity against K. pneumoniae and/or drug-resistant A. baumannii. Two new chemical series with activity against XDR A. baumannii were identified meeting our criteria of potency (EC50 ≤50 μM) and absence of cytotoxicity (HepG2 CC50 ≥100 μM and red blood cell lysis HC50 ≥100 μM). The activity of close analogues of the two chemical series was also determined against A. baumannii clinical isolates. Interpretation: This work provides proof of principle for the screening strategy developed to identify NCEs with antibacterial activity against multidrug-resistant critical priority pathogens such as K. pneumoniae and A. baumannii. The screening and hit selection cascade established here provide an excellent foundation for further screening of new compound libraries to identify high quality starting points for new antibacterial lead generation projects. Funding: BMBF and GARDP.

The impact of H. pylori resistance on patient's treatment failure is a major concern. Therefore, the development of novel or alternative therapies for H. pylori is urgently needed. The purpose of this study was to investigate the molecular interactions of various antimicrobial peptides (AMPs) to H. pylori proteins. We performed the peptide-protein molecular docking using HADDOCK 2.4 webserver. Fourteen AMPs were tested for their binding efficacy against four H. pylori proteins. Simulation of the peptide-protein complex was performed using molecular dynamic software package AMBER20. From molecular docking analysis, five peptides (LL-37, Tilapia piscidin 4, napin, snakin-1 and EcAMP1) showed strong binding interactions against H. pylori proteins. The strongest binding affinity was observed in the interactions between Snakin-1 and PBP2, TP4 and type I HopQ and EcAMP1 and type I HopQ with −11.1, −13.6 and −13.8 kcal/mol, respectively. The dynamic simulation was performed for two complexes (snakin1-PBP2 and EcAMP1-HopQ). Results of the dynamics simulation showed that EcAMP1 had stable interaction and binding to type I HopQ protein without significant structural changes. In conclusion, both results of docking and simulation showed that EcAMP1 might be useful as a potential therapeutic agent for H. pylori treatment. This molecular approach provides deep understanding of the interaction insights between AMPs and H. pylori proteins. It paves the way for the development of novel anti-H. pylori using antimicrobial peptides.

Background: Klebsiella (K.) pneumoniae is a ubiquitous Gram-negative bacterium and a common coloniser of animals and humans. Today, K. pneumoniae is one of the most persistent nosocomial pathogens worldwide and poses a severe threat/burden to public health by causing urinary tract infections, pneumonia and bloodstream infections. Infections mainly affect immunocompromised individuals and hospitalised patients. In recent years, a new type of K. pneumoniae has emerged associated with community-acquired infections such as pyogenic liver abscess in otherwise healthy individuals and is therefore termed hypervirulent K. pneumoniae (hvKp). The aim of this study was the characterisation of K. pneumoniae isolates with properties of hypervirulence from Germany. Methods: A set of 62 potentially hypervirulent K. pneumoniae isolates from human patients was compiled. Inclusion criteria were the presence of at least one determinant that has been previously associated with hypervirulence: (I) clinical manifestation, (II) a positive string test as a marker for hypermucoviscosity, and (III) presence of virulence associated genes rmpA and/or rmpA2 and/or magA. Phenotypic characterisation of the isolates included antimicrobial resistance testing by broth microdilution. Whole genome sequencing (WGS) was performed using Illumina® MiSeq/NextSeq to investigate the genetic repertoire such as multi-locus sequence types (ST), capsule types (K), further virulence associated genes and resistance genes of the collected isolates. For selected isolates long-read sequencing was applied and plasmid sequences with resistance and virulence determinants were compared. Results: WGS analyses confirmed presence of several signature genes for hvKp. Among them, the most prevalent were the siderophore loci iuc and ybt and the capsule regulator genes rmpA and rmpA2. The most dominant ST among the hvKp isolates were ST395 capsule type K2 and ST395 capsule type K5; both have been described previously and were confirmed by our data as multidrug-resistant (MDR) isolates. ST23 capsule type K1 was the second most abundant ST in this study; this ST has been described as commonly associated with hypervirulence. In general, resistance to beta-lactams caused by the production of extended-spectrum beta-lactamases (ESBL) and carbapenemases was observed frequently in our isolates, confirming the threatening rise of MDR-hvKp strains. Conclusions: Our study results show that K. pneumoniae strains that carry several determinants of hypervirulence are present for many years in Germany. The detection of carbapenemase genes and hypervirulence associated genes on the same plasmid is highly problematic and requires intensified screening and molecular surveillance. However, the non-uniform definition of hvKp complicates their detection. Testing for hypermucoviscosity alone is not specific enough to identify hvKp. Thus, we suggest that the classification of hvKp should be applied to isolates that not only fulfil phenotypical criteria (severe clinical manifestations, hypermucoviscosity) but also (I) the presence of at least two virulence loci e.g. iuc and ybt, and (II) the presence of rmpA and/or rmpA2.

Antimicrobial-resistant bacteria are frequently isolated from retail meat and may infect humans. To determine the diversity of antimicrobial-resistant bacteria in Australian retail meat, bacteria were cultured on selective media from raw chicken (n = 244) and pork (n = 160) meat samples obtained from all four major supermarket chains in the ACT/NSW, Australia, between March and June 2021. Antimicrobial susceptibility testing (AST) was performed for 13 critically and 4 highly important antibiotics as categorised by the World Health Organization (WHO) for a wide range of species detected in the meat samples. A total of 288 isolates underwent whole-genome sequencing (WGS) to identify the presence of antimicrobial resistance (AMR) genes, virulence genes, and plasmids. AST testing revealed that 35/288 (12%) of the isolates were found to be multidrug-resistant (MDR). Using WGS data, 232/288 (81%) of the isolates were found to harbour resistance genes for critically or highly important antibiotics. This study reveals a greater diversity of AMR genes in bacteria isolated from retail meat in Australia than previous studies have shown, emphasising the importance of monitoring AMR in not only foodborne pathogenic bacteria, but other species that are capable of transferring AMR genes to pathogenic bacteria.

Abstract Background Bacterial infections in COVID-19 patients, especially those caused by multidrug-resistant gram-negative strains, are associated with increased morbidity, hospital stay and mortality. However, there is limited data on the epidemiology of extended-spectrum β-lactamase (ESBL)-producing bacteria in COVID-19 patients. Here, we assessed the prevalence and the factors associated with ESBL-producing gram-negative bacterial (GNB) infections among severely ill COVID-19 patients admitted in Kenyatta National Hospital (KNH), Kenya. Methods We adopted a descriptive cross-sectional study design for patients admitted between October 2021 and February 2022, purposively recruiting 120 SARS-CoV- 2 infected participants based on clinical presentation. Demographics and clinical characteristics data were collected using structured questionnaires and case report forms. Clinical samples were collected and analyzed by standard microbiological methods in the KNH Microbiology laboratory and the Centre for Microbiology Research, Kenya Medical Research Institute. Results GNB infections prevalence was 40.8%, majorly caused by ESBL—producers (67.3%) predominated by Klebsiella pneumoniae (45.5%). Generally, 73% of the ESBL producers harboured our target ESBL genes, mainly CTX-M-type (59%, 17/29) in K. pneumoniae (76.9%, 20/26). GNB harbouring TEM-type (83%, 10/12) and SHV-type (100%, 7/7) genes showed ESBLs phenotypes and inhibitor resistance, mainly involving clavulanate, but most of them remained susceptible to tazobactam (60%, 6/10). SHV-type genes carrying ESBL producers showed resistance to both cefotaxime (CTX) and ceftazidime (CAZ) (K. pneumoniae), CAZ (E. coli) or CTX (E. cloacae complex and K. pneumoniae). About 87% (20/23) of isolates encoding CTX-M-type β-lactamases displayed CTX/ceftriaxone (CRO) resistance phenotype. About 42% of isolates with CTX-M-type β-lactamases only hydrolyzed ceftazidime (CAZ). Isolates with OXA-type β-lactamases were resistant to CTX, CAZ, CRO, cefepime and aztreonam. Patients with comorbidities were 10 times more likely to have an ESBL-producing GNB infection (aOR = 9.86, 95%CI 1.30 – 74.63, p = 0.003). Conclusion We report a high prevalence of ESBL-GNB infections in severely ill COVID-19 patients, predominantly due to Klebsiella pneumoniae harbouring CTX-M type ESBL genes. The patient’s underlying comorbidities increased the risk of ESBL-producing GNB infection. In COVID-19 pandemic, enhanced systematic and continuous surveillance of ESBL-producing GNB, strict adherence to infection control measures and antimicrobial stewardship policies are warranted in the current study setting.

Abstract Background Patients admitted to intensive care units (ICU) are at risk of Gram-negative bacteria (GNB) infections, especially those caused by multidrug-resistant (MDR) isolates, increasing morbidity, mortality, and healthcare costs. However, epidemiological surveillance data on MDR bacteria to inform infection prevention and control (IPCs) interventions is limited in our study setting. Here we assessed the prevalence and factors associated with GNB infections in ICU- patients admitted in our study setting. Methods This was a hospital-based cross-sectional study among patients admitted to ICU at the Nairobi West Hospital, Kenya, between January and October 2022. Altogether, we recruited 162 patients, excluding those hospitalized for less than 48 h and declining consent, and collected demographics and clinical data by case report form. Blood, wound and throat swab, ascetic tap, stool, urine, tracheal aspirate, and sputum samples were collected cultured. Isolates identity and antimicrobial susceptibility were elucidated using the BD Phoenix system. Results The prevalence of GNB infections was 55.6%, predominated by urinary tract infections (UTIs). We recovered 13 GNB types, with Escherichia coli (33.3%) and Klebsiella pneumoniae (31.1%) as the most common isolates. Factors associated with GNB infections were a history of antibiotic use (aOR = 4.23, p = 0.001), nasogastric tube use (NGT, aOR = 3.04, p = 0.013), respiratory tract (RT, aOR = 5.3, p = 0.005) and cardiovascular (CV, aOR = 5.7, p = 0.024) conditions. 92% of the isolates were MDR,predominantly Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Conclusion We report a high prevalence of MDR-GNB infections, predominated by UTI, in ICU, whereby patients with a history of antibiotic use, using the NGT, and having RT and CV conditions were at increased risk. To improve the management of ICU-admitted patients, continuous education, training, monitoring, evaluation and feedback on infection prevention and control are warranted in our study setting.

Hang Lin,1,2 Cui Zhou,1 Kai-Hang Yu,3 Yi-Shuai Lin,1 Ling-Bo Wang,1 Ying Zhang,1 Shi-Xing Liu,1 Wen-Ya Xu,1 Yao Sun,1 Tie-Li Zhou,1 Jian-Ming Cao,4 Jian-Zhong Ye1 1Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People’s Republic of China; 2School of the First Clinical Medical Sciences, Wenhzou Medical University, Wenzhou, Zhejiang Province, People’s Republic of China; 3Pathology Department, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, People’s Republic of China; 4School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, People’s Republic of ChinaCorrespondence: Tie-Li Zhou; Jian-Zhong Ye, Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang Street, Ouhai District, Wenzhou, 325000, People’s Republic of China, Email wyztli@163.com; jzye89@163.comObjective: Acinetobacter baumannii is a hazardous bacterium that causes hospital-acquired nosocomial infections, and the advent of multidrug-resistant A. baumannii (MDR-AB) strains is concerning. Novel antibacterial therapeutic strategies must be developed. The biological effects of glabridin on MDR-AB were investigated in this study.Methods: The minimum inhibitory concentrations (MICs) of glabridin against eight clinical MDR-AB strains were determined using the broth microdilution technique. Crystal violet staining was used to assess biofilm development, which has significant contribution to bacterial resistance. Swarming motility was measured according to surface growth zone of MDR-AB on LB agar medium. qRT-PCR was used to evaluate the expression of quorum sensing genes abaI and abaR. Glabridin and routinely used therapeutic antimicrobial agents were tested for synergistic action using the checkerboard method.Results: According to our findings, glabridin suppressed MDR-AB growth at high doses (512– 1024 μg/mL). The 1/4 MIC of glabridin significantly decreased MDR-AB biofilm formation by 19.98% (P < 0.05), inhibited MDR-AB motility by 44.27% (P < 0.05), whereas the 1/2 MIC of glabridin dramatically reduced MDR-AB biofilm development by 27.43% (P < 0.01), suppressed MDR-AB motility by 50.64% (P < 0.05). Mechanistically, glabridin substantially downregulated the expression of quorum sensing-related genes abaI and abaR by up to 39.12% (P < 0.001) and 25.19% (P < 0.01), respectively. However, no synergistic effect between glabridin and antibacterial drugs was found.Conclusion: Glabridin might be a quorum sensing inhibitor that inhibits MDR-AB biofilm development and swarming motility.Keywords: Acinetobacter baumannii, multidrug-resistance, glabridin, quorum sensing

The prevalence of carbapenem-resistant P. aeruginosa has dramatically increased over the last decade, and antibiotics alone are not enough to eradicate infections caused by this opportunistic pathogen. Phage therapy is a fresh treatment that can be administered under compassionate use, particularly against chronic cases. However, it is necessary to thoroughly characterize the virus before therapeutic application. Our work describes the discovery of the novel sequenced bacteriophage, vB_PaeP-F1Pa, containing an integrase, performs a phylogenetical analysis, describes its stability at a physiological pH and temperature, latent period (40 min), and burst size (394 ± 166 particles per bacterial cell), and demonstrates its ability to infect MDR and XDR P. aeruginosa strains. Moreover, this novel bacteriophage was able to inhibit the growth of bacteria inside preformed biofilms. The present study offers a road map to analyze essential areas for successful phage therapy against MDR and XDR P. aeruginosa infections, and shows that a phage containing an integrase is also able to show good in vitro results, indicating that it is very important to perform a genomic analysis before any clinical use, in order to prevent adverse effects in patients.

Tsegahun Asfaw,1 Deribew Genetu,2 Demissew Shenkute,1 Tassew Tefera Shenkutie,1 Yosef Eshetie Amare,3 Habtemariam Alekaw Habteweld,4 Berhanu Yitayew1 1Department of Medical Laboratory Science, Debre Berhan University, Debre Berhan, Ethiopia; 2Department of Medical Laboratory Science, Injibara University, Injibara, Ethiopia; 3Departments of Biomedical Science, Debre Berhan University, Debre Berhan, Ethiopia; 4Departments of Pharmacy, Debre Berhan University, Debre Berhan, EthiopiaCorrespondence: Tsegahun Asfaw, Email tsegahun.asfaw12@gmail.comBackground: Bacterial contamination of milk is a primary culprit for causing foodborne illnesses, presenting a significant health hazard for millions of individuals around the globe. The level and variety of microorganisms present in raw milk determine its degree of contamination and the potential health risks it poses.Methods: A cross-sectional survey was conducted from February to August. A questionnaire was used to collect data on socio-demographic characteristics and hygiene practices from milk distributors and traders. Raw milk, yoghurt, swabs from milk containers and drinking cups were collected and processed for bacterial isolation and identification, antibiotic susceptibility testing, MDR screening and confirmation, ESBL screening and confirmation. Finally, all data were pooled and analyzed using SPSS software version 25.Results: A total of 120 samples of fresh milk, yogurt and cotton swabs from milk containers and cups were collected. A total of 80 bacterial isolates were isolated from 120 samples. Among the bacteria isolated, S. aureus 17 (21.3%), E. coli 17 (21.3%), S. epidermidis 14 (17.5%), Klebsiella spp. 9 (11.3%) and Salmonella spp. 7 (8.8%) were detected most often. High rate of contamination was observed in fresh milk 23 (28.8%) and yogurt 23 (28.8%). All isolates were resistant to at least one antibiotic tested. Comparatively, high rates of resistance were observed in all isolates to the most commonly prescribed antibiotics in Ethiopia. However, lower rates of resistance have been observed for recently introduced antibiotics in Ethiopia. Of the isolates, 20 (25.0%) were resistant to eight or more antibiotics. While 16 (20.0%), 12 (15.0%), 9 (11.3%) isolates were resistant to two, three and five antibiotics, respectively. Of the bacteria isolated, 52/80 (65.0%) were MDR, 25/49 (51.0%) were screened for ESBL production, and 20/49 (40.8%) isolates were confirmed as ESBL producer.Conclusion: This study showed a high rate of bacterial isolates along with MDR and ESBL-producing strains in raw milk, yoghurt, milk container swabs and drinking cup swab samples, associated with poor hygiene and sanitation practices.Keywords: bacterial contamination, multidrug-resistance, extended-spectrum beta-lactamase, raw milk, yoghurt, milk contact surface

Shan Chen,1 Houming Liu,1 Tianpin Li,1 Wenjie Lai,1 Lei Liu,1 Youchun Xu,2 Jiuxin Qu1 1Department of Clinical Laboratory, Shenzhen Third People’s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, People’s Republic of China; 2Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, People’s Republic of ChinaCorrespondence: Jiuxin Qu, Department of Clinical Laboratory, Shenzhen Third People’s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, People’s Republic of China, Email Qujiuxin@163.com Youchun Xu, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, People’s Republic of China, Email CYX040198@163.comBackground: The currently used conventional susceptibility testing for drug-resistant Mycobacterium tuberculosis (M.TB) is limited due to being time-consuming and having low efficiency. Herein, we propose the use of a microfluidic-based method to rapidly detect drug-resistant gene mutations using Kompetitive Allele-Specific PCR (KASP).Methods: A total of 300 clinical samples were collected, and DNA extraction was performed using the “isoChip®” Mycobacterium detection kit. Phenotypic susceptibility testing and Sanger sequencing were performed to sequence the PCR products. Allele-specific primers targeting 37 gene mutation sites were designed, and a microfluidic chip (KASP) was constructed using 112 reaction chambers to simultaneously detect multiple mutations. Chip validation was performed using clinical samples.Results: Phenotypic susceptibility of clinical isolates revealed 38 rifampicin (RIF)-resistant, 64 isoniazid (INH)-resistant, 48 streptomycin (SM)-resistant and 23 ethambutol (EMB)-resistant strains, as well as 33 multi-drug-resistant TB (MDR-TB) strains and 20 strains fully resistant to all four drugs. Optimization of the chip-based detection system for drug resistance detection showed satisfactory specificity and maximum fluorescence at a DNA concentration of 1× 101 copies/μL. Further analysis revealed that 76.32% of the RIF-resistant strains harbored rpoB gene mutations (sensitivity, 76.32%; specificity 100%), 60.93% of the INH-resistant strains had katG gene mutations (sensitivity, 60.93%; specificity, 100%), 66.66% of the SM-resistant strains carried drug resistance gene mutations (sensitivity, 66.66%; specificity, 99.2%), and 69.56% of the EMB-resistant strains had embB gene mutations (sensitivity, 69.56%; specificity, 100%). Further, the overall agreement between the microfluidic chip and Sanger sequencing was satisfactory, with a turnaround time of the microfluidic chip was approximately 2 hours, much shorter than the conventional DST method.Conclusion: The proposed microfluidic-based KASP assay provides a cost-effective and convenient method for detecting mutations associated with drug resistance in M. tuberculosis. It represents a promising alternative to the traditional DST method, with satisfactory sensitivity and specificity and a much shorter turnaround time.Graphical Abstract: Keywords: Mycobacterium tuberculosis, multidrug-resistance, drug resistance, resistance-conferring gene mutations, polymerase chain reaction, microfluidic analytical techniques, Sanger sequencing

IntroductionAcinetobacter spp., in particular A. baumannii, are opportunistic pathogens linked to nosocomial pneumonia (particularly ventilator-associated pneumonia), central-line catheter-associated blood stream infections, meningitis, urinary tract infections, surgical-site infections, and other types of wound infections. A. baumannii is able to acquire or upregulate various resistance determinants, making it frequently multidrug-resistant, and contributing to increased mortality and morbidity. Data on the epidemiology, levels, and trends of antimicrobial resistance of Acinetobacter spp. in clinical settings is scarce in the Gulf Cooperation Council (GCC) and Middle East and North Africa (MENA) regions.MethodsA retrospective 12-year analysis of 17,564 non-duplicate diagnostic Acinetobacter spp. isolates from the United Arab Emirates (UAE) was conducted. Data was generated at 317 surveillance sites by routine patient care during 2010–2021, collected by trained personnel and reported by participating surveillance sites to the UAE National AMR Surveillance program. Data analysis was conducted with WHONET.1ResultsSpecies belonging to the A. calcoaceticus-baumannii complex were mostly reported (86.7%). They were most commonly isolated from urine (32.9%), sputum (29.0%), and soft tissue (25.1%). Resistance trends to antibiotics from different classes during the surveillance period showed a decreasing trend. Specifically, there was a significant decrease in resistance to imipenem, meropenem, and amikacin. Resistance was lowest among Acinetobacter species to both colistin and tigecycline. The percentages of multidrug-resistant (MDR) and possibly extensively drug-resistant (XDR) isolates was reduced by almost half between the beginning of the study in 2010 and its culmination in 2021. Carbapenem-resistant Acinetobacter spp. (CRAB) was associated with a higher mortality (RR: 5.7), a higher admission to ICU (RR 3.3), and an increased length of stay (LOS; 13 excess inpatient days per CRAB case), as compared to Carbapenem-susceptible Acinetobacter spp.ConclusionCarbapenem-resistant Acinetobacter spp. are associated with poorer clinical outcomes, and higher associated costs, as compared to carbapenem-susceptible Acinetobacter spp. A decreasing trend of MDR Acinetobacter spp., as well as resistance to all antibiotic classes under surveillance was observed during 2010 to 2021. Further studies are needed to explore the reasons and underlying factors leading to this remarkable decrease of resistance over time.

IntroductionPseudomonas is a group of ubiquitous non-fermenting Gram-negative bacteria (NFGNB). Of the several species associated with humans, Pseudomonas aeruginosa (PA) can acclimate to diverse environments. The global frequency of PA infections is rising and is complicated by this organism's high intrinsic and acquired resistance to several clinically relevant antibiotics. Data on the epidemiology, levels, and trends of antimicrobial resistance of PA in clinical settings in the MENA/GCC region is scarce.MethodsA retrospective 12-year analysis of 56,618 non-duplicate diagnostic Pseudomonas spp. from the United Arab Emirates (UAE) was conducted. Data was generated at 317 surveillance sites by routine patient care during 2010–2021, collected by trained personnel and reported by participating surveillance sites to the UAE National antimicrobial resistance (AMR) Surveillance program. Data analysis was conducted with WHONET (https://whonet.org/).ResultsAmong the total isolates (N = 56,618), the majority were PA (95.6%). Data on nationality revealed 44.1% were UAE nationals. Most isolates were from soft tissue (55.7%), followed by respiratory tract (26.7%). PA was more commonly found among inpatients than among outpatients, followed by ICUs. PA showed a horizontal trend for resistance to fluoroquinolones, 3rd- and 4th-generation cephalosporins, and decreasing trends of resistance for aminoglycosides and meropenem. The highest percentage of multidrug resistant (MDR) isolates was reported in 2011 at 35.6%. As an overall trend, the percentage of MDR, extensively drug-resistant (XDR), and possible pandrug-resistant (PDR) isolates generally declined over the study period. Carbapenem-resistant PA (CRPA) were associated with a higher mortality (RR: 2.7), increased admission to ICU (RR: 2.3), and increased length of stay (LOS) (12 excess inpatient days per case), as compared to carbapenem-susceptible PA (CSPA).ConclusionThe resistance trends in Pseudomonas species in the UAE indicated a decline in AMR and in percentages of Pseudomonas isolates with MDR and XDR profiles. The sustained Pseudomonas spp. circulation particularly in the hospital settings highlights the importance of surveillance techniques, infection control strategies, and stewardship to limit the continued dissemination. This data also shows that CRPA are associated with higher mortality, increased ICU admission rates, and a longer hospitalization, thus higher costs due to increased number of in-hospital and ICU days.

Pseudomonas aeruginosa is a main cause of nosocomial infections and is classified as a priority critical pathogen of global concern. Multidrug resistance and virulence genes attributed to the pathogenicity of the organism has resulted in failed therapies, linked to increased morbidity and mortality in infected patients. The aim of this study was to determine the virulence genes and multidrug resistant P.aeruginosa in clinical specimens from a secondary health care center laboratory in Lagos, Nigeria. Methodology: A total of three hundred and sixty-seven clinical samples were examined with conventional methods and Microbact GNB12A. Forty- seven (47) P. aeruginosa strains were identified. Antimicrobial susceptibility test was performed by the standard disk diffusion method following CLSI guidelines. Identification of P. aeruginosa was done by amplification of oprL and oprI genes. Monoplex and multiplex PCR assays were used for detecting virulence genes (lasB, toxA, exoU and nan1). Descriptive statistical methods were used to analyze the distribution of P. aeruginosa by sample sources, MDR patterns by number of isolates and virulence gene carriage by MDR (≥3classes of antibiotics). Results: A total of forty-seven (47) isolates were confirmed as P. aeruginosa. The isolates showed pan-resistance to cefuroxime and ceftazidime. An elevated level of resistance was also seen in amoxycillin-clavulanic acid, ceftriaxone, cefixime and meropenem. Susceptibility to Amikacin was 95.7 %. Multidrug resistance was seen in forty (85.1 %) of the isolates. P. aeruginosa (100 %) were confirmed with oprL and 74.5 % oprI genes. All isolates (100 %) had lasB, toxA and exoS virulence genes while nan1 was detected in 19.1 % isolates. Conclusions: Diverse and multiple virulence genes were distributed among the multidrug resistant isolates. Understanding the factors contributing to pathogenicity and antibiotic resistance will aid in the treatment of infection. It will also promote judicious use of antimicrobials.

Background: Bacterial infections in COVID-19 patients, especially those caused by multidrug-resistant gram-negative strains, are associated with increased morbidity, hospital stay and mortality. However, there is limited data on the epidemiology of extended-spectrum β-lactamase (ESBL)-producing bacteria in COVID-19 patients. Here, we assessed the prevalence and the factors associated with ESBL-producing gram-negative bacterial (GNB) infections among severely ill COVID-19 patients admitted in Kenyatta National Hospital (KNH), Kenya. Methods: We adopted a descriptive cross-sectional study design for patients admitted between October 2021 and February 2022, purposively recruiting 120 SARS-CoV- 2 infected participants based on clinical presentation. Demographics and clinical characteristics data were collected using structured questionnaires and case report forms. Clinical samples were collected and analyzed by standard microbiological methods in the KNH Microbiology laboratory and the Centre for Microbiology Research, Kenya Medical Research Institute. Results: GNB infections prevalence was 40.8%, majorly caused by ESBL—producers (67.3%) predominated by Klebsiella pneumoniae (45.5%). Generally, 73% of the ESBL producers harboured our target ESBL genes, mainly CTX-M-type (59%, 17/29) in K. pneumoniae (76.9%, 20/26). GNB harbouring TEM-type (83%, 10/12) and SHV-type (100%, 7/7) genes showed ESBLs phenotypes and inhibitor resistance, mainly involving clavulanate, but most of them remained susceptible to tazobactam (60%, 6/10). SHV-type genes carrying ESBL producers showed resistance to both cefotaxime (CTX) and ceftazidime (CAZ) (K. pneumoniae), CAZ (E. coli) or CTX (E. cloacae complex and K. pneumoniae). About 87% (20/23) of isolates encoding CTX-M-type β-lactamases displayed CTX/ceftriaxone (CRO) resistance phenotype. About 42% of isolates with CTX-M-type β-lactamases only hydrolyzed ceftazidime (CAZ). Isolates with OXA-type β-lactamases were resistant to CTX, CAZ, CRO, cefepime and aztreonam. Patients with comorbidities were 10 times more likely to have an ESBL-producing GNB infection (aOR = 9.86, 95%CI 1.30 – 74.63, p = 0.003). Conclusion: We report a high prevalence of ESBL-GNB infections in severely ill COVID-19 patients, predominantly due to Klebsiella pneumoniae harbouring CTX-M type ESBL genes. The patient's underlying comorbidities increased the risk of ESBL-producing GNB infection. In COVID-19 pandemic, enhanced systematic and continuous surveillance of ESBL-producing GNB, strict adherence to infection control measures and antimicrobial stewardship policies are warranted in the current study setting. [ABSTRACT FROM AUTHOR]

Nosocomial outbreaks of multidrug-resistant (MDR) Enterobacter cloacae complex (ECC) are often reported worldwide, mostly associated with a small number of multilocus-sequence types of E. hormaechei and E. cloacae strains. In Europe, the largest clonal outbreak of blaNDM-1-producing ECC has been recently reported, involving an ST182 E. hormaechei strain in a Greek teaching hospital. In the current study, we aimed to further investigate the genetic make-up of two representative outbreak isolates. Comparative genomics of whole genome sequences (WGS) was performed, including whole genome-based taxonomic analysis and in silico prediction of virulence determinants of the bacterial cell surface, plasmids, antibiotic resistance genes and virulence factors present on genomic islands. The enterobacterial common antigen and the colanic antigen of the cell surface were identified in both isolates, being similar to the gene clusters of the E. hormaechei ATCC 49162 and E. cloacae ATCC 13047 type strains, whereas the two strains possessed different gene clusters encoding lipopolysaccharide O-antigens. Other virulence factors of the bacterial cell surface, such as flagella, fimbriae and pili, were also predicted to be encoded by gene clusters similar to those found in Enterobacter spp. and other Enterobacterales. Secretion systems and toxin–antitoxin systems, which also contribute to pathogenicity, were identified. Both isolates harboured resistance genes to multiple antimicrobial classes, including β-lactams, aminoglycosides, quinolones, chloramphenicol, trimethoprim, sulfonamides and fosfomycin; they carried blaTEM-1, blaOXA-1, blaNDM-1, and one of them also carried blaCTXM-14, blaCTXM-15 and blaLAP-2 plasmidic alleles. Our comprehensive analysis of the WGS assemblies revealed that blaNDM-1-producing outbreak isolates possess components of the bacterial cell surface as well as genomic islands, harbouring resistance genes to several antimicrobial classes and various virulence factors. Differences in the plasmids carrying β-lactamase genes between the two strains have also shown diverse modes of acquisition and an ongoing evolution of these mobile elements. [ABSTRACT FROM AUTHOR]

Background: Patients admitted to intensive care units (ICU) are at risk of Gram-negative bacteria (GNB) infections, especially those caused by multidrug-resistant (MDR) isolates, increasing morbidity, mortality, and healthcare costs. However, epidemiological surveillance data on MDR bacteria to inform infection prevention and control (IPCs) interventions is limited in our study setting. Here we assessed the prevalence and factors associated with GNB infections in ICU- patients admitted in our study setting. Methods: This was a hospital-based cross-sectional study among patients admitted to ICU at the Nairobi West Hospital, Kenya, between January and October 2022. Altogether, we recruited 162 patients, excluding those hospitalized for less than 48 h and declining consent, and collected demographics and clinical data by case report form. Blood, wound and throat swab, ascetic tap, stool, urine, tracheal aspirate, and sputum samples were collected cultured. Isolates identity and antimicrobial susceptibility were elucidated using the BD Phoenix system. Results: The prevalence of GNB infections was 55.6%, predominated by urinary tract infections (UTIs). We recovered 13 GNB types, with Escherichia coli (33.3%) and Klebsiella pneumoniae (31.1%) as the most common isolates. Factors associated with GNB infections were a history of antibiotic use (aOR = 4.23, p = 0.001), nasogastric tube use (NGT, aOR = 3.04, p = 0.013), respiratory tract (RT, aOR = 5.3, p = 0.005) and cardiovascular (CV, aOR = 5.7, p = 0.024) conditions. 92% of the isolates were MDR,predominantly Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Conclusion: We report a high prevalence of MDR-GNB infections, predominated by UTI, in ICU, whereby patients with a history of antibiotic use, using the NGT, and having RT and CV conditions were at increased risk. To improve the management of ICU-admitted patients, continuous education, training, monitoring, evaluation and feedback on infection prevention and control are warranted in our study setting. [ABSTRACT FROM AUTHOR]

Bacteriophages were discovered in early 20th century. However, the interest in bacteriophage research was reduced with the discovery of antibiotics. With the increasing number of infections due to multidrug-resistant (MDR) organisms, the potential usefulness of bacteriophages as therapeutic agents has been re-evaluated. In this review, we found that more than 30 lytic bacteriophages that infect Acinetobacter species have been characterised. These are mainly members of Caudovirales, with genome sizes ranging from 31 kb to 234 kb and G+C contents ranging from 33.5% to 45.5%. The host range can be as low as < 10% of all tested Acinetobacter strains. Fourteen published murine trials indicated positive outcomes in bacteriophage-treated groups. Only two case reports were pertaining to the use of bacteriophages in the treatment of Acinetobacter infections in humans; in both cases, the infections were resolved with bacteriophage therapy. The use of bacteriophages has been associated with reduced Acinetobacter burden in the environment, as shown in two studies. The major limitation of bacteriophage therapy is its highly selective host strain. In conclusion, the potential usefulness of bacteriophage therapy for the treatment of MDR Acinetobacter species has been documented only in limited studies and more research is needed prior to its extensive use in clinical practice. [ABSTRACT FROM AUTHOR]

The Enterobacterales order is a massive group of Gram-negative bacteria comprised of pathogenic and nonpathogenic members, including beneficial commensal gut microbiota. The pathogenic members produce several pathogenic or virulence factors that enhance their pathogenic properties and increase the severity of the infection. The members of Enterobacterales can also develop resistance against the common antimicrobial agents, a phenomenon called antimicrobial resistance (AMR). Many pathogenic Enterobacterales members are known to possess antimicrobial resistance. This review discusses the virulence factors, pathogenicity, and infections caused by multidrug-resistant Enterobacterales, especially E. coli and some other bacterial species sharing similarities with the Enterobacterales members. We also discuss both conventional and modern approaches used to combat the infections caused by them. Understanding the virulence factors produced by the pathogenic bacteria will help develop novel strategies and methods to treat infections caused by them. [ABSTRACT FROM AUTHOR]

Urinary tract infections (UTIs) are the leading cause of hospitalization due to bacterial infection, and the frequency of multidrug-resistant Escherichia coli isolates from these infections is increasing worldwide. The current study aims to isolate and characterize antibiotic-resistant Escherichia coli and their antibiogram typing from urine samples of humans. From April to December 2019, a total of 60 human urine samples were collected aseptically and treated to primary isolation by propagation in nutrient broth followed by culture on various agar media. Gram's staining, string techniques, biochemical characterization, PCR, and Sanger sequencing were performed to confirm E. coli. The Kirby-Bauer disk diffusion technique was used to test the susceptibility of all bacterial strains to thirteen typically prescribed antibiotics. The overall prevalence of E. coli in UTIs was 66.67%. Three variations were noted in E. coli, all of which were single substitutions (A>T, C>T, and T>A). Phylogenetic analysis of the 16S rRNA revealed that the E. coli discovered in this study belonged to the genus Escherichia, but was distinct from those identified in other countries. The antibiograms revealed that all the isolates (100%) were resistant to penicillin, ampicillin, and amoxicillin; 94.87% to doxycycline; 79.16% to gentamycin; 75.48% to ciprofloxacin; 73.07% to erythromycin; 71.66% to levofloxacin; 47.36% to ceftriaxone; and 46.66% to tetracycline. In contrast, all E. coli strains were sensitive to amikacin (95%), vancomycin (92.50%), and azithromycin (92.50%). People with a urinary tract infection (UTI) often have multidrug-resistant E. coli in their urine samples, which calls for a one-health strategy to deal with this rapidly changing condition. [ J Adv Biotechnol Exp Ther 2023; 6(1.000): 172-183]

Pseudomonas aeruginosa is an expedient Gram-negative bacterium, which is characterized by its ability to acquire antimicrobial resistance. In this study, 56 unrepeatable carbapenem-resistant P. aeruginosa isolates were gathered from various clinical sources from hospitals in Cairo and Mansoura universities. The isolates exhibited diminished susceptibility towards carbapenems, quinolones, aminoglycosides and chloramphenicol by using disc diffusion method. Carbapenemase production was confirmed among the isolates, where all the 56 P. aeruginosa isolates harboured carbapenemase genes including blaVIM (43 isolates), blaKPC (38 isolates), blaNDM-1 (17 isolates), blaIMP (16 isolates) and blaOXA-48 (15 isolates). Among the isolates, 13 carried only one carbapenemase gene, while 43 isolates carried multiple carbapenemase genes. MCR-1 production was confirmed in 10 of the tested isolates by detecting the mcr-1 gene encoding for the colistin resistance. Enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) evaluation showed that the tested isolates were unrelated to each other. Therefore, this study rises the danger of emergence of MDR P. aeruginosa resistant to carbapenems coupled with other antimicrobials including colistin, which is regarded as the last reservoir for the management of infections caused by MDR Gram-negative pathogens. Early inspection of resistance patterns in MDR organisms is an important tool to control and prevent infections via limiting the spread of these pathogens.

Amani Alnimr Department of Medical Microbiology, King Fahad Hospital of the University, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi ArabiaCorrespondence: Amani Alnimr, Department of Medical Microbiology, King Fahad Hospital of the University, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia, Tel +966133335130, Email amalnimr@iau.edu.saAbstract: Ralstonia spp. is an emerging, non-fermentative Gram-negative rod that demonstrates multidrug resistance. Herein, four cases of bloodstream infections (BSI) caused by R. mannitolilytica or R. pickettii are presented. All the cases had comorbidities that predisposed them to this opportunistic infection. The microbiological assessment showed carbapenemase genes carried out in two strains with minimal inhibitory concentrations > 32 μg/mL to imipenem and meropenem. Fluoroquinolones and trimethoprim-sulphamethoxazole were the most potent agents showing activity against 3/4 strains (75%), although treatment should be susceptibility-dependent for each strain. This case series highlights the possibility of co-infection by a rare organism during the COVID-19 pandemic and the importance of the readiness of diagnostic laboratories to support the diagnosis of uncommon pathogens.Keywords: multidrug-resistance, bacteremia, bacillary, OXA-48, carbapenemase

Abstract Background Klebsiella pneumoniae, which is frequently associated with hospital- and community-acquired infections, contains multidrug-resistant (MDR), hypervirulent (hv), non-MDR/non-hv as well as convergent representatives. It is known that mostly international high-risk clonal lineages including sequence types (ST) 11, 147, 258, and 307 drive their global spread. ST395, which was first reported in the context of a carbapenemase-associated outbreak in France in 2010, is a less well-characterized, yet emerging clonal lineage. Methods We computationally analyzed a large collection of K. pneumoniae ST395 genomes (n = 297) both sequenced in this study and reported previously. By applying multiple bioinformatics tools, we investigated the core-genome phylogeny and evolution of ST395 as well as distribution of accessory genome elements associated with antibiotic resistance and virulence features. Results Clustering of the core-SNP alignment revealed four major clades with eight smaller subclades. The subclades likely evolved through large chromosomal recombination, which involved different K. pneumoniae donors and affected, inter alia, capsule and lipopolysaccharide antigen biosynthesis regions. Most genomes contained acquired resistance genes to extended-spectrum cephalosporins, carbapenems, and other antibiotic classes carried by multiple plasmid types, and many were positive for hypervirulence markers, including the siderophore aerobactin. The detection of “hybrid” resistance and virulence plasmids suggests the occurrence of the convergent ST395 pathotype. Conclusions To the best of our knowledge, this is the first study that investigated a large international collection of K. pneumoniae ST395 genomes and elucidated phylogenetics and detailed genomic characteristics of this emerging high-risk clonal lineage.

Antimicrobial resistance is a critical challenge due to the overuse of conventional antimicrobials, and alternative solutions are urgently needed. This study investigates the efficacy of compounds derived from lactic acid bacteria (LAB) fermentation combined with antibiotics against multidrug-resistant pathogens isolated from clinical cases in a hospital setting. Strains of Escherichia coli, Klebsiella pneumoniae, and Enterococcus faecium and faecalis were isolated and selected from blood, respiratory, and urine samples. They were tested against the fermentation products from the Ingulados LAB collection (BAL5, BAL6, BAL8, BAL13, and BAL16), recognized for their antimicrobial efficacy against veterinary pathogens. The activity against multidrug-resistant (MDR) pathogens was evaluated initially, followed by synergy tests using checkerboard assays and subsequent analysis. Bioinformatic assessments and supernatant treatments were performed to characterize the nature of the compounds responsible for the antimicrobial activity. Notably, BAL16 exhibited significant growth inhibition against multidrug-resistant E. faecium. Synergy tests highlighted its combined activity with tetracycline through FICI and surface analysis and bioinformatic analysis unveiled the protein fraction containing bacteriocins as the underlying mechanism. This study highlights BAL16 fermentation products potential as valuable antimicrobial agents against MDR E. faecium infections, attributed to bacteriocins. Further in-depth studies are necessary for complete bacteriocin characterization.