Coexistence of bla NDM-5 and tet(X4) in international high-risk Escherichia coli clone ST648 of human origin in China

Advances in drug resistance and resistance mechanisms of four colorectal cancer-associated gut microbiota

Colorectal cancer (CRC) is a common malignant tumor in the gastrointestinal tract with inconspicuous early symptoms, high morbidity and mortality, and poor prognosis. Gut microbiota are present in the human intestinal system and have certain functions, which include the integrity of the epithelial barrier and the enhancement of protective immune responses. The etiology of CRC is numerous and complex, including poor lifestyle and dietary habits, and instability of the gut microbiota, which is considered to be one of the major factors in the development of CRC, includes mainly Bacteroides fragilis, Fusobacterium nucleatum, Escherichia coli, and Enterococcus faecalis. Enrichment of these bacteria in CRC tumor tissues may increase other pro-inflammatory opportunistic pathogens and decrease butyrate-producing bacteria, leading to an imbalance in intestinal homeostasis (dysbiosis) and ultimately tumor formation. Antibiotic-induced changes in the gut microbiota affect tissue utilization and redox homeostasis of macronutrients and micronutrients. However, the long-term use and abuse of antibiotics has made the problem of drug resistance a difficult problem that currently plagues the regulation of gut microbiota, as well as a complicated issue in the prevention and treatment of CRC. In this review, we elucidated the drug resistance of four CRC-associated gut microbiota, namely Bacteroides fragilis, Fusobacterium nucleatum, Escherichia coli, and Enterococcus faecalis, and discussed the common and different aspects of the resistance mechanisms of the four gut microbiota, with the aim of providing a basis for the prevention and control of CRC.

Multidrug resistance and virulence profile of the commensal Proteus mirabilis isolated from a native Iraqi frozen chicken carcass

This study aimed to determine the prevalence of Proteus mirabilis in frozen chicken carcass from local slaughterhouse. It assesses the activities of nine antimicrobial agents and the presence of antimicrobial resistance genes and virulence genes. Thirty samples were collected from five local Iraqi companies. and then the antibiotic-resistance genes and virulence factor-related genes were detected via polymerase chain reaction (PCR). The results revealed that Nine P. mirabilis isolates were recovered, and the majority of the isolates were resistant to both nalidixic acid and azithromycin at a ratio of (100 %), followed by trimethoprim-sulfamethoxazole (sul1) (88.8 %), whereas the isolates were susceptible to imipenem and meropenem, and both ceftazidime and cefotaxime were efficient at a ratio of (88.8 %). All the isolates (100 %) were resistant to at least three classes of antibiotics and were classified as multidrug resistant. The PCR results indicated that the most common resistance genes were DNA Gyrase Subunit A Gene (gyrA) (100 %), Dihydropteroate Synthase Gene (sul1) (88.8 %), and Florenicol Resistance Gene (floR) (88.8 %), followed by Aminoglycoside N-Acetyltransferase Gene (acc (6')-lb) (44.4 %) and Macrolide Phosphotransferase Gene (mphA) (33.3 %). In addition, the virulence genes Zinc Metalloprotease A Gene (zapA), Uridine Monophosphate Synthase Gene (uraC), Histone-Modifying Protein A Gene (hpmA), Flagellin A Gene (flaA), Anti-Sigma Factor RsbA Gene (rsbA), and Multidrug Resistance Protein A Gene (mrpA) were found in the same proportion (100 %) of all P. mirabilis isolates. Our study emphasized that Proteus mirabilis has a high frequency of antibiotic resistance as a multidrug resistance pattern and furthermore demonstrated a high level of virulence factor gene detection, which might be a threat to food safety and human health. The phylogenetic tree analysis of the P. mirabilis isolates from chicken meat revealed high similarity to the database strain.

Targeted next-generation sequencing enhances precision and rapid detection in healthcare-associated infection Surveillance: Unveiling multidrug-resistant colonization in ICUs

Objectives

This study aims to evaluate the potential advantages of targeted next-generation sequencing (tNGS) over conventional bacterial culture methods for pathogen detection in hospital-associated infections (HAIs).

Methods

All EICU medical staff and all medical staff from the Physical Examination Centre completed a questionnaire. Nasopharyngeal specimens were collected from medical staff who met all of the inclusion criteria and none of the exclusion criteria. EICU medical staff provided 2 samples each, while Physical Examination Centre staff provided 1 sample each. For EICU medical staff, one of their two nasopharyngeal swabs was subjected to tNGS testing, and the other to bacterial culture testing. For the PEC staff, their nasopharyngeal swabs were subjected to tNGS testing. Additionally, six pairs of spectacles and six keyboards used by EICU medical staff were randomly selected, and the surfaces were swabbed with sterile swabs for tNGS testing.

Results

In 23 nasal swab samples from EICU group, tNGS detected 14 species of microorganism in 29 instances within 19 h. Bacterial culture detected 2 species of microorganism in 4 instances, 2 positive samples within 19 h and confirmed another 2 positive samples within 69 h. A total of 42 samples with 14 different microorganism species were collected from the nasopharyngeal swabs of 23 EICU members and 15 PEC members. Among them, 29 cases (69 %) of 14 different microorganisms were detected in EICU staff, with an average of 1.3 microorganism species detected per person, while 13 cases (28 %) of 6 different microorganisms were detected in PEC staff, with an average of 0.9 microorganism species detected per person. The most common colonizing bacteria included Staphylococcus aureus, Acinetobacter baumannii, and Klebsiella spp. Compared to bacterial culture, tNGS offers advantages in monitoring HAIs, including a broad range of detectable microorganisms, high sensitivity of results, and shorter reporting time for positive results. Bacteria colonizing the EICU carry more antibiotic resistance genes.

Conclusions

tNGS outperforms conventional culture in healthcare-associated infection surveillance, with higher sensitivity and accelerated pathogen identification. Simultaneously, tNGS revealed extensive colonization of multidrug-resistant (MDR) pathogens (e.g., Acinetobacter baumannii, MRSA) in EICU environments, highlighting its utility in monitoring complex antimicrobial resistance patterns.

Binding assays enable discovery of Tet(X) inhibitors that combat tetracycline destructase resistance

The Tet(X) flavin-dependent monooxygenases enable tetracycline antibiotic resistance by catalysing inactivating hydroxylation, so preventing inhibition of bacterial ribosomes. Tet(X) resistance is growing rapidly, threatening the efficacy of important last-resort tetracyclines such as tigecycline. Tet(X) inhibitors have potential to protect tetracyclines in combination therapies, but their discovery has been hampered by lack of high-throughput assays. We report the development of an efficient fluorescence polarisation Tet(X) binding assay employing a tetramethylrhodamine-glycyl-minocycline conjugate that enables inhibitor discovery. The assay was applied to tetracycline substrates and reported inhibitors, providing insight into their binding modes. Screening of a bioactive molecule library identified novel Tet(X) inhibitors, including psychoactive phenothiazine derivatives and the 5-HT4 agonist tegaserod, the activities of which were validated by turnover assays. Crystallographic studies of Tet(X4)-inhibitor complexes reveal two new inhibitor binding modes, importantly providing evidence for active site binding of Tet(X) inhibitors that do not share structural similarity with tetracycline substrates. In some cases, potentiation of tigecycline activity was observed in bacteria expressing Tet(X4). The combined results provide non-tetracycline scaffolds for development of potent Tet(X) inhibitors and highlight the need to evaluate the impact of non-antibiotics on antimicrobial resistance.

Antibiotic resistance and virulence patterns of O25 and O16 serogroups in uropathogenic Escherichia coli

OBJECTIVE

This study investigates antibiotic resistance patterns, virulence factors, and phylogenetic groups of O25 and O16 serogroups in uropathogenic Escherichia coli (UPEC) isolates from kidney transplant recipients (KTPs) and non-KTPs. The presence of serogroups O25 and O16, resistance genes (e.g., blaCTX-M, blaTEM), and virulence factors (e.g., fimH, PAI) were determined using PCR. Phylogenetic groups were identified via quadruplex PCR, and genetic diversity was assessed using ERIC-PCR.

RESULTS

A total of 111 E. coli isolates were examined in the present study. The O-serotyping results indicated that 18% and 3.6% of isolates were positive for O25 and O16 serogroup, respectively. In serogroup O25, the highest resistance rates were observed for nalidixic acid and cotrimoxazole, whereas in serogroup O16, the highest resistance rates were against cotrimoxazole and ampicillin-sulbactam. ESBL production was identified in 30% of O25 and 25% of O16 isolates. O25 isolates belonged to phylogenetic group B2, whereas O16 isolates were grouped in B1. ERIC-PCR revealed significant genetic diversity among isolates. The O25 serogroup is prevalent and closely associated with high antibiotic resistance and virulence, suggesting its critical role in UTI pathogenesis in transplant patients. These findings underscore the importance of monitoring resistance patterns and developing targeted therapeutic and preventive strategies for managing UPEC infections.

Emergence of highly virulent multidrug and extensively drug resistant Escherichia coli and Klebsiella pneumoniae in buffalo subclinical mastitis cases

This study aimed to characterize virulence and antibiotic resistance genes in multidrug-resistant (MDR) and extensively drug-resistant (XDR) Escherichia coli and Klebsiella pneumoniae isolated from cases of subclinical mastitis (SCM) in buffaloes. A cross-sectional study was conducted on 1540 quarter milk samples collected from 385 buffaloes. Milk samples were screened using the California Mastitis Test and Modified Whiteside Test. Positive samples underwent bacterial culture, biochemical tests, biofilm detection and molecular analysis for pathogen identification and detection of virulence, resistance, and extended-spectrum beta-lactamase (ESBL) genes. The prevalence of SCM was 67.9% (1046/1540) at the quarter level and 80.8% (311/385) at the animal level. E. coli was identified in 9.5% (146/1540) of the samples, while K. pneumoniae was detected in 9.09% (140/1540). Virulence genes, such as stx1 (27.4%), and resistance genes, including aac(3)-iv (77.4%) and tetA (76.7%), exhibited higher prevalence. Additionally, β-lactamase genes, notably blaTEM (67.1%), and ESBL genes, such as blaCTX-M1, were detected. Biofilm formation was detected in 83.6% (122/146) of E. coli isolates and 75.7% (106/140) of K. pneumoniae isolates. Antimicrobial susceptibility testing revealed significant resistance to ampicillin, amoxicillin-clavulanic acid, and aminoglycosides. MDR was observed in 31.5% of E. coli and 39.3% of K. pneumoniae isolates, with XDR rates of 8.9% and 12.9%, respectively. These findings underscore the alarming spread of resistant pathogens in SCM-affected buffaloes, emphasizing the urgent need for ongoing surveillance and targeted intervention strategies.

Genetic variations underlying aminoglycoside resistance in antibiotic-induced Mycobacterium intracellulare mutants

Mycobacterium avium complex (MAC) is an emerging pathogen leading to public health concerns in developing and developed countries, particularly among immunocompromised individuals and patients with structural lung diseases. Current clinical guidelines recommend combination antibiotic therapy for treating MAC pulmonary disease (MAC-PD). However, the rising prevalence of antibiotic resistance poses significant challenges, including treatment failure and clinical recurrence. A deeper understanding of the mechanisms underlying MAC antibiotic resistance is essential to improve treatment outcomes. This study investigates the genetic variations associated with aminoglycoside resistance in an antibiotic-induced Mycobacterium intracellulare mutant derived from a clinical strain. Whole-genome analysis identified seven mutations in the aminoglycoside-resistant mutant, including single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). Key genetic alterations included a frameshift variant in a gene encoding a secreted protein antigen, missense mutations in rpsL and rsmG, and synonymous and in-frame deletion variants in srfAB and mtrB, respectively. These findings highlight the complex genetic landscape of aminoglycoside resistance in M. intracellulare. Understanding these resistance determinants provides valuable insights for developing diagnostic tools to detect drug-resistant MAC strains and optimizing therapeutic strategies for managing MAC infections in clinical practice.

Risk Factors for Development and Mortality of Carbapenem-Resistant Pseudomonas aeruginosa Bloodstream Infection in a Chinese Teaching Hospital: A Seven-Year Retrospective Study

Objective

Pseudomonas aeruginosa (P. aeruginosa) is a gram-negative opportunistic pathogen, which can cause acute and chronic infections, often resulting in high mortality. The aim of this study was to investigate the risk factors for the development and mortality of patients with carbapenem-resistant P. aeruginosa bloodstream infection (CRPA BSI).

Methods

A total of 112 patients with CRPA BSI and 112 patients with carbapenem-sensitive P. aeruginosa (CSPA) BSI were included from a Chinese teaching hospital from January 2017 to December 2023 in this retrospective cohort study. The detection rate, antimicrobial susceptibility of P. aeruginosa and clinical characteristics of these patients were investigated. Multivariable logistic regression analysis was used to identify risk factors for the development and outcomes of CRPA BSI.

Results

In the past 7 years, 7480 blood samples of P. aeruginosa were cultured in the hospital. The detection rates of CRPA, multidrug resistant P. aeruginosa (MDRPA), and difficult-to-treat resistant P. aeruginosa (DTRPA) BSI increased annually (26% to 47%, 10% to 36% and 5% to 15%, respectively). CRPA showed high resistance to conventional antibiotics. Chronic lung disease (OR 3.953, 95% CI 1.131-13.812), transplantation (OR 2.837, 95% CI 1.036-7.770), multi-organ failure (OR 4.815, 95% CI 1.949-11.894), pre-infection within CRPA (OR 9.239, 95% CI 3.441-24.803), and exposure to carbapenems within 90 days (OR 2.734, 95% CI 1.052 -7.106) were independent risk factors for the development of CRPA bacteremia. Sepsis or septic shock (OR 8.774, 95% CI 3.140-24.515, p = 0.001) were independent risk factors of mortality.

Conclusion

Chronic lung disease, transplantation, multi-organ failure, prior CRPA infection, and prior carbapenems exposure are independent risk factors for the development of CRPA bacteremia. Sepsis or septic shock increases 28-day mortality. To investigate the molecular mechanisms of carbapenem-resistance of P. aeruginosa, standardize antibiotic usage, and assess risk factors for the development and mortality of CRPA BSI are beneficial to control infection and reduce death.

Unveiling resistance patterns, kmt1 sequence analyses, virulence traits, and antibiotic resistance genes of multidrug-resistant Pasteurella multocida retrieved from poultry and rabbits

Pasteurella multocida is incriminated in fowl cholera in poultry and snuffles in rabbits, causing significant economic losses in the poultry industry worldwide. This study investigated the prevalence, kmt1 gene sequencing, antibiogram, pathogenicity, and PCR detection of the virulence and resistance genes of P. multocida recovered from chickens, ducks, and rabbits. Approximately 150 samples were collected from diseased chickens, ducks, and rabbits (50 for each) from commercial farms in Ismailia government, Egypt. The collected samples were bacteriologically examined, and the recovered isolates were subsequently subjected to kmt1 gene sequencing, antibiogram, pathogenicity test, and PCR-based detection of virulence and antibiotic resistance genes. The overall prevalence of P. multocida was 20% (30/150). The highest prevalence was recorded in rabbits (24%; 12/50), followed by ducks (20%; 10/50) and chickens (16%; 8/50). The lung was the most predominant infected organ. Moreover, the kmt1 phylogenetic analysis emphasized that the tested P. multocida strains presented remarkable genetic identity with other P. multocida strains from the USA, Denmark, China, India, and Iran. Chloramphenicol and ciprofloxacin exhibited promising results in treating P. multocida. Moreover, the prevalence of oma87, ptfA, luxS, tadG, and nanB virulence genes was 100%, 86.7%, 76.6%, 73.3%, and 56.7% respectively. Herein, 13.3% of the tested strains were multidrug-resistant (MDR) to 5 antibiotic classes and carried blaROB-1 and tetH genes. Besides, 10% of the tested P. multocida strains were extensively drug resistant (XDR) to 7 antibiotic classes and harbored the blaROB-1, tetH, and ermX genes. Moreover, 10% of the recovered P. multocida strains were MDR to 5 antibiotic classes and had tetH and ermX genes. Pathogenicity test revealed that the mortality rate was 20% at 1 day post-infection, reaching its highest point (100%) at 2 days post-infection. Briefly, this study highlights the occurrence of MDR and XDR P. multocida in domestic birds and rabbits, revealing a public health threat. The oma87, ptfA, luxS, and tadG virulence genes and the blaROB-1, tetH, and ermX antibiotic resistance genes are usually associated with emerging MDR P. multocida strains.

Seroprevalence of brucellosis in camels and humans in the Al-Qassim region of Saudi Arabia and its implications for public health

Brucellosis is a significant zoonotic disease caused by intracellular, gram-negative bacteria from the genus Brucella. Although camels are classified as secondary hosts for Brucella species, they are among the most susceptible and vulnerable animals to brucellosis, particularly Brucella abortus (B. abortus) and Brucella melitensis (B. melitensis). The present study aimed to investigate the epidemiology of camel brucellosis as a zoonotic disease by determining the seroprevalence of brucellosis in both camels and humans, assessing potential risk factors (e.g., age, size, and location), and conducting molecular characterization of Brucella spp. associated with abortion in camels. The Rose Bengal Test (RBT), Antigen Rapid Brucella Antibody Test (ARBT), indirect enzyme-linked immunosorbent assay (I-ELISA), and complement fixation test (CFT) were used to detect brucellosis in both camels and humans. Additionally, a molecular method using polymerase chain reaction was used as a confirmatory technique. A total of 625 camel serum samples and 100 human serum samples were collected in sterile vacuum tubes from various camel farms and individuals across different localities in the Al Qassim region. Additionally, samples from 10 confirmed Brucella-infected camels (including the uterus and supramammary lymph nodes) were analyzed. The results indicated that the overall prevalence of brucellosis in camel sera was 9.72%, as determined by RBT, and 8.16%, as determined by ARBT. In contrast, the overall prevalence of brucellosis in human sera from febrile patients was found to be 17% via RBT. Notably, 57.98% of camel sera that tested positive for Brucella antibodies via RBT were also positive according to I-ELISA and CFT. Furthermore, 42.1%, 70.58%, and 47.05% of human sera that were positive for Brucella antibodies as determined by RBT were also positive according to I-ELISA and CFT, respectively. The highest seropositivity for camel brucellosis was observed in female camels, particularly in the Unaizah area of the Qassim region and among the Homr breed. The prevalence of human brucellosis was highest among females and individuals who consumed raw milk. At the molecular level, B. melitensis biovar 3 was detected in the examined tissues. In conclusion, intervention measures are vital for reducing brucellosis in humans and camels. Public awareness campaigns should highlight the importance of protective clothing when handling aborted she-camels and the need to boil or pasteurize milk. Additionally, studies should differentiate between vaccinated and nonvaccinated camels, and standardizing serological tests for diagnosing brucellosis should be prioritized.

First report of MDR virulent Pseudomonas aeruginosa in apparently healthy Japanese quail (Coturnix japonica) in Bangladesh

Pseudomonas aeruginosa (P. aeruginosa) is a major pathogen associated conditions like septicaemia, respiratory disorders, and diarrhoea in poultry, particularly in Japanese quail (Coturnix japonica). The infection causes huge economical losses due to its high transmissibility, mortality and zoonotic potential. This study aimed to isolate, identify, detect virulence genes, and profile multidrug resistance (MDR) of P. aeruginosa from Japanese quail. Oral and rectal swabs were collected from 110 apparently healthy quail birds across various districts in Bangladesh. Bacterial isolation and identification were performed using cultural, morphological, biochemical, and polymerase chain reaction (PCR) methods. Antibiotic susceptibility was assessed using the disc diffusion method, and virulence genes were detected through PCR. Multivariable logistic regression was used to identify risk factors for P. aeruginosa infection. Both conventional and PCR methods revealed that 25 (22.73%) of the quail birds were positive for P. aeruginosa. The results showed that quail birds in Narsingdi were five times more likely to harbor Pseudomonas species (OR: 5.02; 95% CI: 1.34-18.84) compared to those in Mymensingh Sadar. Additionally, quail birds younger than eight weeks had nearly six times higher odds (OR: 5.93; 95% CI: 1.96-17.91) of carrying Pseudomonas compared to older birds. Female quail birds had almost four times higher odds (OR: 3.77; 95% CI: 1.30-10.93) of harboring Pseudomonas species than males. All 25 P. aeruginosa isolates exhibited multi drug-resistance (MDR) patterns. Virulence gene analysis revealed the consistent presence of exoA and rhlR in all isolates, while exoS, exoY, rhlI, and rhlAB showed variable distribution. The high prevalence of MDR and virulent P. aeruginosa in apparently healthy quail birds particularly in Mymensingh and Dhaka divisions, highlights the urgent need for a comprehensive 'One Health' approach to proactively address and mitigate the potential risk this organism poses to both quail and human populations.

Assessment of biofilm formation, antibiotic resistance patterns, and the prevalence of adhesion-related genes in clinical Staphylococcus aureus isolates

Background

This study aimed to evaluate the biofilm formation abilities of clinical Staphylococcus aureus strains, assess their antibiotic susceptibility patterns, and identify the prevalence of adhesion-associated genes.

Methodology

In this study, a total of 60 S. aureus strains were collected from urine, pus, wounds, blood, body fluid, and sputum in health centers affiliated with Abadan University of Medical Sciences, Iran. Strains were identified via microbiological methods and polymerase chain reaction (PCR) to target the nuc gene. Antibiotic susceptibility testing (AST) was conducted via the disc diffusion method. Methicillin-resistant S. aureus (MRSA) strains were identified by cefoxitin disc diffusion and PCR targeting the mecA gene. Biofilm formation was assessed via a microtiter plate assay, and the prevalence of adhesion-encoding genes was evaluated via PCR. The data were analyzed in Excel and SPSS via statistical methods, with P-values <0.05 considered significant.

Results

Using AST, daptomycin and linezolid were the most effective antibiotics (100 % susceptibility rate). According to the results of the cefoxitin disc test, 48.3 % (n = 29/60) of the strains were MRSA. All the MRSA strains harbored the mecA gene. In total, 32 % of the strains were biofilm producers. Moreover, 56.2 %, 28.1 %, and 15.6 % of the strains produced weak, moderate, and strong biofilms, respectively. There were no significant differences between the MRSA and MSSA strains in terms of the association of biofilm formation with antibiotic resistance except for erythromycin (P-value = 0.0087), gentamicin (P-value = 0.0009), and penicillin (P-value = 0.0009). The most prevalent biofilm-encoding genes were icaA (76.7 %), followed by icaD (70 %), clfA (65.0 %), and fnbA (53.3 %).

Conclusion

This study identified MRSA strains with biofilm-forming abilities that possess adhesion-associated genes. The most prevalent biofilm-encoding gene was icaA. To prevent further spread of these strains, regional preventive measures are needed.

Exploring phenotypic and genotypic diversity among methicillin-resistant, vancomycin-resistant, and sensitive Staphylococcus aureus

BACKGROUND

Methicillin-Resistant Staphylococcus aureus (MRSA) is a global concern owing to the increasing prevalence of multidrug-resistant (MDR) strains. Vancomycin has been the primary treatment for MRSA; however, Vancomycin-resistant strains are being increasingly reported worldwide. Therefore, comparative studies are essential to support antimicrobial stewardship and improving clinical management. Ultimately, the findings from this study are expected to inform treatment strategies and guide public health interventions effectively.

MATERIAL AND METHODS

This study investigated the prevalence, antimicrobial resistance, and virulence characteristics of Vancomycin-sensitive S. aureus (VSSA) and Vancomycin-resistant S. aureus (VRSA) within MRSA strains. By employing a combination of phenotypic methods, such as antimicrobial susceptibility testing, and genotypic techniques, including molecular typing and identification of virulence genes, we obtained comprehensive insights into VRSA and VSSA profiles.

RESULTS

Of 250 clinical samples, 62 (24.8%) were S. aureus and 27 (43.5%) were identified as MRSA. All MRSA isolates exhibited MDR patterns. Most MRSA strains were VSSA (20/27, 74.1%), while 7 (25.9%) were VRSA. The VRSA isolates showed more antimicrobial resistance than VSSA isolates; however, the VRSA isolates had less virulence than VSSA isolates. Linezolid was the most effective treatment, with a 3.7% resistance rate. A higher percentage of biofilm-producing MRSA (96.3%) was confirmed by both phenotypic and genotypic methods. All isolates, except one VRSA, showed multi-virulence patterns (harbored more than 3 virulence genes). High diversity and low clonality (D-value = 0.99) were found in both VSSA and VRSA. Based on our correlation findings, the emergence of vancomycin resistance could modify the association between antimicrobial resistance and virulence, potentially affecting the pathogenic profile of these strains. The study also revealed complex interactions among host factors (including age and gender), sample origin, antimicrobial resistance, biofilm production, and virulence genes.

CONCLUSION

This study highlights the alarming spread of MRSA and VRSA, which show significant resistance and virulence.

Antimicrobial resistance genes and associated mobile genetic elements in Escherichia coli from human, animal and environment

The global rise of antimicrobial resistance (AMR) poses a significant threat to human health. The environment plays an essential role in transmission of antimicrobial resistance genes (ARGs) between human and animal. Bacterial communities harbour diverse ARGs, carried by mobile genetic elements (MGEs) like plasmids and insertion sequences (ISs). Here, a total of 2199 Escherichia coli (E. coli) whole genome sequences from human, animal, bird and environment were retrieved globally to investigate ARG prevalence and assess their genetic framework. The study highlights how the genetic background including plasmids, IS elements and transposons surrounding ARGs influences their transmission potential. The maximum number of ARGs was found in United Kingdom followed by USA, majorly in human hosts. However, IS-associated ARGs were most prevalent in bird hosts. ARGs like aph(6)-ld, aph(3″)-lb, blaCTX-M, blaNDM were widespread across all hosts. Tn2 was the most prevalent, majorly carried by IncFIB plasmids. The IS26 and ISVsa3 carried diverse ARGs, primarily linked to aminoglycoside and β-lactam resistance. The combinations like mph(A)_IS6100 and blaNDM-5_IS5 showed fixed IS-ARG associations. ARGs like blaNDM, blaCTX-M variants displayed strong association with IS elements. The study highlights possible mechanism of transmission due to close proximity of AMR genes to MGEs, offering promising strategies to combat AMR by predicting and addressing future resistance determinants.

Prevalence and molecular characterization of ESBL-producing Escherichia coli isolated from broiler chicken and their respective farms environment in Malaysia

BACKGROUND

Extended spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) is an increasing public health threat. This study aimed to determine the prevalence and characterization of ESBL-producing Escherichia coli (E. coli) isolated from broiler chicken and their farm environment, in Kelantan Malaysia.

METHODS

Escherichia coli was isolated from 453 collected samples, including 210 cloacal swabs and 243 environmental samples. The antimicrobial susceptibility profile of the E. coli isolates was assessed for sixteen antibiotics using the disc diffusion method. The E. coli isolates were evaluated for phenotypic ESBL production using modified double disc synergy. After extraction of genomic DNA, ESBL resistance genes, phylogenetic group, and virulence genes were detected by PCR using appropriate primers. ESBL genes were further confirmed by sequencing. The molecular typing of E. coli strains was determined by Multilocus Sequence Typing (MLST).

RESULTS

A total of 93.8% (425/453) E. coli were isolated from the collected samples. Out of 334 E. coli isolates screened, 14.7% (49/334) were phenotypically ESBL producers. All the ESBL-EC were resistant to tetracycline, ciprofloxacin, and ampicillin. Thus, 100% of the ESBL-EC were multidrug resistant. Of the ESBL-EC 81.6% were positive for at least one ESBL encoding gene. The most prevalent ESBL gene detected was blaTEM (77.6%; 38/49) followed by blaCTX-M (32.7%; 16/49) and blaSHV (18.4%; 9/49). The majority of ESBL-EC belonged to phylogenic groups A followed by B1 accounting for 44.9% and 12.2%, respectively. The most frequently identified sequence types were ST10 (n = 3) and ST206 (n = 3). The most detected virulence genes in the E. coli isolates were astA (33.3%; 22/66) followed by iss (15.2%; 10/66).

CONCLUSIONS

Our results show both broiler chicken and their respective farms environment were reservoirs of multi-drug resistant ESBL-producing E. coli and ESBL resistance genes.

Detection and characterization of multidrug resistant Escherichia coli carrying virulence gene isolated from broilers in Bangladesh

BACKGROUND

The emergence and dissemination of multidrug resistant (MDR) bacteria pose a severe threat to public health by limiting clinical treatment and prophylactic options.

OBJECTIVES

This study investigates the prevalence of Escherichia coli in broilers, their phenotypic antimicrobial resistance (AMR) profiles and the presence of virulence-associated genes (VAGs) and antimicrobial resistance genes (ARGs) using polymerase chain reaction (PCR).

MATERIALS AND METHODS

A total of 216 pooled cloacal samples were collected from 1080 broilers across six districts of Bangladesh. Each pooled sample comprised randomly selected cloacal swabs from five birds per farm. E. coli isolates were identified using standard bacteriological approach, followed by biochemical assays and PCR. Antimicrobial susceptibility was assessed using the Kirby-Bauer disc diffusion method, and the presence of ARGs and VAGs was determined via PCR. Five selected isolates were partially sequenced for five VAGs using Sanger sequencing.

RESULTS

A total of 177 E. coli isolates (81.94%, 95% confidence interval: 76.24%-86.53%) were identified. The isolates showed the highest resistance to ampicillin (93.79%), followed by tetracycline (91.53%), erythromycin (89.27%) and ciprofloxacin (87%). Conversely, ceftriaxone (80.79%) showed highest susceptibility, followed by gentamicin (37.29%) and neomycin (31.07%). All isolates were MDR, with a multiple antibiotic resistance indexes were <0.3. A significant percentage (16.38%) of E. coli isolates were MDR to five antimicrobial classes and harboured blaTEM, sul1, ere (A), tetA, tetB and tetC genes. The highest prevalent ARGs were blaTEM (88.14%) followed by ere (A) (83.62%) and sul 1 (72.32%). The prevalence of VAGs was astA (56.50%), iucD (31.07%), iss (21.47%), irp2 (15.82%) and cva/cvi (3.39%), respectively.

CONCLUSIONS

This study highlights the presence of ARGs contributing to the development of MDR in E. coli carrying VAGs in broilers. Effective monitoring and surveillance of antimicrobial usage in poultry production systems are urgently required to prevent emergence and dissemination of AMR.

Epidemiological and molecular investigations of Salmonella isolated from duck farms in southwest and around area of Shandong, China

Salmonella is a zoonotic pathogen posing a serious risk to the farming industry and public health due to food animals serving as reservoirs for future contamination and spread of Salmonella. The present study is designed to monitor the contamination status of Salmonella in duck farms and the main control points during breeding. 160 strains of duck-derived Salmonella were isolated from the 736 samples (cloacal swabs, feces, water, feed, soil, air and dead duck embryos) collected in southwest Shandong Province and the province's surrounding area. The percentage of Salmonella-positive samples collected was 21.74 % (160/736), and the greatest prevalence from duck embryo samples (40.00 %, 36/90). These Salmonella were classified into 23 serotypes depending on their O and H antigens, in which S. Typhimurium (30.15 %), S. Kottbus (13.97 %) and S. Enteritidis (10.29 %) were the prevailing serotypes. Subsequently, the molecular subtyping was done. Clustered regularly interspaced short palindromic repeats (CRISPR) analysis showed that 41 strains of S. Typhimurium and 14 strains of S. Enteritidis were classified into 13 and 3 genotypes, respectively. 19 S. Kottbus isolates from different sources featured ST1546, ST198, ST321, and ST1690 by multilocus sequence typing (MLST) analysis, among which ST1546 belongs to S. Kottbus was a new ST. The minimum spanning tree analysis based on the two CRISPR loci and seven MLST loci from all S. Typhimurium, S. Enteritidis and S. Kottbus isolates revealed that duck embryos, feed and water were key control points to the spread of Salmonella along the breeding chain. Meanwhile, the emergence of S. Kottbus in duck flocks was considered a potential public health hazard.

Distribution of virulence genes and antimicrobial resistance of Escherichia coli isolated from hospitalized neonates: A multi-center study across China

Background

Escherichia coli is the most common gram-negative pathogen to cause neonatal infections. Contemporary virulence characterization and antimicrobial resistance (AMR) data of neonatal E. coli isolates in China are limited.

Methods

A total of 159 E. coli strains isolated from neonates were collected and classified into invasive and non-invasive infection groups, according to their site of origin. The presence of virulence genes was determined using polymerase chain reaction (PCR). All the strains were subjected to antimicrobial susceptibility testing using the broth dilution method.

Results

The top three virulence genes with the highest detection rates were fimH (90.6 %), iutA (88.7 %), and kspMT II (88.1 %). The prevalences of fyuA (p = 0.023), kpsMT K1 (p = 0.019), ibeA (p < 0.001), and iroN (p = 0.027) were significantly higher in the invasive infection group than in the non-invasive infection group. Resistance to ceftazixime, sulfamethoxazole/trimethoprim, and ciprofloxacin was 75.5 %, 65.4 %, and 48.4 %, respectively. Lower rates of resistance to ceftazidime (p = 0.022), cefepime (p = 0.005), ticarcillin/clavulanic acid (p = 0.020) and aztreonam (p = 0.001) were observed in the invasive infection group compared to the non-invasive infection group. The number of virulence genes carried by E. coli was positively correlated with the number of antibiotics to which the isolates were resistant (r = 0.71, p = 0.016), and a specific virulence gene was associated with resistance to various species of antibiotics.

Conclusions

Neonatal E. coli isolates carried multiple virulence genes and were highly resistant to antibiotics. Further studies are needed to understand the molecular mechanisms underlying the association between virulence and AMR.

The Occurrence of Colistin Resistance in Potential Lactic Acid Bacteria of Food-Producing Animals in India

The overuse of colistin, the last-resort antibiotic, has led to the emergence of colistin-resistant bacteria, which is a major concern. Lactic acid bacteria which are generally regarded as safe are known to be reservoirs of antibiotic resistance that possibly pose a threat to human and animal health. Therefore, this study assessed the prevalence of colistin antimicrobial resistance in livestock in India, that is lactic acid bacteria in healthy chickens, sheep, beef, and swine of Mysore. Diverse phenotypic and genotypic colistin resistance were examined among the lactic acid bacterial species (n = 84) isolated from chicken (n = 44), sheep (n = 16), beef (n = 14), and swine (n = 10). Hi-comb, double-disk diffusion tests, Minimum Inhibitory Concentration (MIC), and biofilm formation were assessed for phenotypic colistin resistance. Specific primers for colistin-resistant genes were used for the determination of genotypic colistin resistance. Around 20%, 18%, and 1% were colistin-resistant Lactobacillus, Enterococcus, and Pediococcus species, respectively. Among these, 66.67% exhibited MDR phenotypes, including colistin antibiotic. The identified resistant isolates are Levilactobacillus brevis LBA and LBB (2), Limosilactobacillus fermentum LBF (1), and Pediococcus acidilactici CHBI (1). The mcr-1 and mcr-3 genes were detected in Levilactobacillus brevis LBA, LBB, and Pediococcus acidilactici CHBI isolated from chicken and sheep intestines respectively. The study identified colistin resistance determinants in lactobacilli from food animals, emphasizing the need for enhanced surveillance and monitoring of resistance spread. These findings underscore colistin resistance as a significant medical concern and should be integrated into India's ongoing antimicrobial resistance monitoring programs.

Large-scale bacterial genomic and metagenomic analysis reveals Pseudomonas aeruginosa as potential ancestral source of tigecycline resistance gene cluster tmexCD-toprJ

BACKGROUND

The global dissemination of the multidrug resistance efflux pump gene cluster tmexCD-toprJ has greatly weakened the effects of multiple antibiotics, including tigecycline. However, the potential origin and transmission mechanisms of the gene cluster remain unclear.

METHODS

Here, we concluded a comprehensive bioinformatics analysis on integrated 73,498 bacterial genomes, including Pseudomonas spp., Klebsiella spp., Aeromonas spp., Proteus spp., and Citrobacter spp., along with 1,152 long-read metagenomic datasets to trace the origin and propagation of tmexCD-toprJ.

RESULTS

Our results demonstrated that tmexCD-toprJ was predominantly found in Pseudomonas aeruginosa sourced from human hosts in Asian countries and North American countries. Phylogenetic and genomic feature analyses showed that tmexCD-toprJ was likely evolved from mexCD-oprJ of some special clones of P. aeruginosa. Furthermore, metagenomic analysis confirmed that P. aeruginosa is the only potential ancestral bacterium for tmexCD-toprJ. A putative mobile genetic structure harboring tmexCD-toprJ, int-int-hp-hp-tnfxB-tmexCD-toprJ, was the predominant genetic context of tmexCD-toprJ across various bacterial genera, suggesting that the two integrase genes play a pivotal role in the horizontal transmission of tmexCD-toprJ.

CONCLUSIONS

Based on these findings, it is almost certain that the tmexCD-toprJ gene cluster was derived from P. aeruginosa and further spread to other bacteria.

Prevalence, antimicrobial susceptibility profiles and resistant gene identification of bovine subclinical mastitis pathogens in Bangladesh

Subclinical mastitis (SCM), a silent threat in the dairy sector of Bangladesh poses a significant economic impact and serves as a potential source of infection for healthy cows, hindering efforts to achieve milk self-sufficiency. Despite the importance of this issue, limited research has been conducted on mastitis in Sylhet region of Bangladesh. This study aimed to investigate the molecular prevalence, antimicrobial susceptibility profile and resistant genes detection on pathogens (Staphylococcus aureus, Escherichia coli, and Klebsiella pneumoniae) causing SCM. In a cross-sectional study utilizing convenience sampling, 325 milk samples were collected from apparently healthy dairy cows. Initially, SCM was detected using the modified Whiteside test (MWST) method. Suspected positive samples were then subjected to bacteriological culture and standard biochemical assays, followed by molecular identification through polymerase chain reaction (PCR). Finally, antimicrobial susceptibility testing was conducted on all PCR-positive samples using the Kirby-Bauer disk diffusion method on Mueller-Hinton agar. In the Sylhet district, the prevalence of SCM was 64.92 % (211 out of 325) at the individual animal level and 82.69 % (43 out of 52) at the herd level. Among the SCM-positive animals, S . aureus was found in 31.75 % (67 out of 211) of cases, E . coli in 81.99 % (173 out of 211), and K . pneumoniae in 66.82 % (141 out of 211). K . pneumoniae had the highest prevalence at 60 % in Zakiganj, S . aureus at 45 % in Zakiganj, and E . coli at 72 % in Bishwanath Upazila. Extended spectrum beta lactamase (ESBL) genes bla TEM , bla OXA, bla CTX-M1, bla CTX-M2, MultiCase DHA were identified. Additionally, antibiotic resistance genes tet(A), AAC (3)-iv, and Sul1 were also detected. The pathogens exhibited resistance to Penicillins (ampicillin, amoxicillin), Cephems (cefuroxime, ceftazidime), and Tetracyclines (tetracycline). However, all three bacteria were highly sensitive to meropenem, amikacin, gentamicin, ciprofloxacin, and sulfamethoxazole-trimethoprim. These findings highlight the critical need for targeted antimicrobial stewardship and effective control measures to mitigate the impact of SCM on dairy production and animal health in the Sylhet region of Bangladesh.

A unique combination of natural fatty acids from Hermetia illucens fly larvae fat effectively combats virulence factors and biofilms of MDR hypervirulent mucoviscus Klebsiella pneumoniae strains by increasing Lewis acid-base/van der Waals interactions in bacterial wall membranes

Introduction

Hypervirulent Klebsiella pneumoniae (hvKp) and carbapenem-resistant K. pneumoniae (CR-Kp) are rapidly emerging as opportunistic pathogens that have a global impact leading to a significant increase in mortality rates among clinical patients. Anti-virulence strategies that target bacterial behavior, such as adhesion and biofilm formation, have been proposed as alternatives to biocidal antibiotic treatments to reduce the rapid emergence of bacterial resistance. The main objective of this study was to examine the efficacy of fatty acid-enriched extract (AWME3) derived from the fat of Black Soldier Fly larvae (Hermetia illucens) in fighting against biofilms of multi-drug resistant (MDR) and highly virulent Klebsiella pneumoniae (hvKp) pathogens. Additionally, the study also aimed to investigate the potential mechanisms underlying this effect.

Methods

Crystal violet (CV) and ethidium bromide (EtBr) assays show how AWME3 affects the formation of mixed and mature biofilms by the KP ATCC BAA-2473, KPi1627, and KPM9 strains. AWME3 has shown exceptional efficacy in combating the hypermucoviscosity (HMV) virulent factors of KPi1627 and KPM9 strains when tested using the string assay. The rudimentary motility of MDR KPM9 and KP ATCC BAA-2473 strains was detected through swimming, swarming, and twitching assays. The cell wall membrane disturbances induced by AWME3 were detected by light and scanning electron microscopy and further validated by an increase in the bacterial cell wall permeability and Lewis acid-base/van der Waals characteristics of K. pneumoniae strains tested by MATS (microbial adhesion to solvents) method.

Results

After being exposed to 0.5 MIC (0.125 mg/ml) of AWME3, a significant reduction in the rudimentary motility of MDR KPM9 and KP ATCC BAA-2473 strains, whereas the treated bacterial strains exhibited motility between 4.23 ± 0.25 and 4.47 ± 0.25 mm, while the non-treated control groups showed significantly higher motility ranging from 8.5 ± 0.5 to 10.5 ± 0.5 mm.

Conclusion

In conclusion, this study demonstrates the exceptional capability of the natural AWME3 extract enriched with a unique combination of fatty acids to effectively eliminate the biofilms formed by the highly drug-resistant and highly virulent K. pneumoniae (hvKp) pathogens. Our results highlight the opportunity to control and minimize the rapid emergence of bacterial resistance through the treatment using AWME3 of biofilm-associated infections caused by hvKp and CRKp pathogens.

Complete genome sequence, phenotypic correlation and pangenome analysis of uropathogenic Klebsiella spp

Urinary tract infections (UTI) by antibiotic resistant and virulent K. pneumoniae are a growing concern. Understanding the genome and validating the genomic profile along with pangenome analysis will facilitate surveillance of high-risk clones of K. pneumoniae to underpin management strategies toward early detection. The present study aims to correlate resistome with phenotypic antimicrobial resistance and virulome with pathogenicity in Klebsiella spp. The present study aimed to perform complete genome sequences of Klebsiella spp. and to analyse the correlation of resistome with phenotypic antimicrobial resistance and virulome with pathogenicity. To understand the resistome, pangenome and virulome in the Klebsiella spp, the ResFinder, CARD, IS Finder, PlasmidFinder, PHASTER, Roary, VFDB were used. The phenotypic susceptibility profiling identified the uropathogenic kp3 to exhibit multi drug resistance. The resistome and in vitro antimicrobial profiling showed concordance with all the tested antibiotics against the study strains. Hypermucoviscosity was not observed for any of the test isolates; this phenotypic character matches perfectly with the absence of rmpA and magA genes. To the best of our knowledge, this is the first report on the presence of ste, stf, stc and sti major fimbrial operons of Salmonella enterica serotype Typhimurium in K. pneumoniae genome. The study identifies the discordance of virulome and virulence in Klebsiella spp. The complete genome analysis and phenotypic correlation identify uropathogenic K. pneumoniae kp3 as a carbapenem-resistant and virulent pathogen. The Pangenome of K. pneumoniae was open suggesting high genetic diversity. Diverse K serotypes were observed. Sequence typing reveals the prevalence of K. pneumoniae high-risk clones in UTI catheterised patients. The study also highlights the concordance of resistome and in vitro susceptibility tests. Importantly, the study identifies the necessity of virulome and phenotypic virulence markers for timely diagnosis and immediate treatment for the management of high-risk K. pneumoniae clones.

Colistin-, cefepime-, and levofloxacin-resistant Salmonella enterica serovars isolated from Egyptian chicken carcasses

OBJECTIVES

The emergence of multidrug-resistant (MDR) Salmonella strains, especially resistant ones toward critically important antimicrobial classes such as fluoroquinolones and third- and fourth-generation cephalosporins, is a growing public health concern. The current study, therefore, aimed to determine the prevalence, and existence of virulence genes (invA, stn, and spvC genes), antimicrobial resistance profiles, and the presence of β-lactamase resistance genes (blaOXA, blaCTX-M1, blaSHV, and blaTEM) in Salmonella strains isolated from native chicken carcasses in Egypt marketed in Mansoura, Egypt, as well as spotlight the risk of isolated MDR, colistin-, cefepime-, and levofloxacin-resistant Salmonella enterica serovars to public health.

METHODS

One hundred fifty freshly dressed native chicken carcasses were collected from different poultry shops in Mansoura City, Egypt between July 2022 and November 2022. Salmonella isolation was performed using standard bacteriological techniques, including pre-enrichment in buffered peptone water (BPW), selective enrichment in Rappaport Vassiliadis broth (RVS), and cultivating on the surface of xylose-lysine-desoxycholate (XLD) agar. All suspected Salmonella colonies were subjected to biochemical tests, serological identification using slide agglutination test, and Polymerase Chain Reaction (PCR) targeting the invasion A gene (invA; Salmonella marker gene). Afterward, all molecularly verified isolates were screened for the presence of virulence genes (stn and spvC). The antimicrobial susceptibility testing for isolated Salmonella strains towards the 16 antimicrobial agents tested was analyzed by Kirby-Bauer disc diffusion method, except for colistin, in which the minimum inhibition concentration (MIC) was determined by broth microdilution technique. Furthermore, 82 cefotaxime-resistant Salmonella isolates were tested using multiplex PCR targeting the β-lactamase resistance genes, including blaOXA, blaCTX-M1, blaSHV, and blaTEM genes.

RESULTS

Salmonella enterica species were molecularly confirmed via the invA Salmonella marker gene in 18% (27/150) of the freshly dressed native chicken carcasses. Twelve Salmonella serotypes were identified among 129 confirmed Salmonella isolates with the most predominant serotypes were S. Kentucky, S. Enteritidis, S. Typhimurium, and S. Molade with an incidence of 19.4% (25/129), 17.1% (22/129), 17.1% (22/129), and 10.9% (14/129), respectively. All the identified Salmonella isolates (n = 129) were positive for both invA and stn genes, while only 31.8% (41/129) of isolates were positive for the spvC gene. One hundred twenty-one (93.8%) of the 129 Salmonella-verified isolates were resistant to at least three antibiotics. Interestingly, 3.9%, 14.7%, and 75.2% of isolates were categorized into pan-drug-resistant, extensively drug-resistant, and multidrug-resistant, respectively. The average MAR index for the 129 isolates tested was 0.505. Exactly, 82.2%, 82.2%, 63.6%, 51.9%, 50.4%, 48.8%, 11.6%, and 10.1% of isolated Salmonella strains were resistant to cefepime, colistin, cefotaxime, ceftazidime/clavulanic acid, levofloxacin, ciprofloxacin, azithromycin, and meropenem, respectively. Thirty-one out (37.8%) of the 82 cefotaxime-resistant Salmonella isolates were β-lactamase producers with the blaTEM as the most predominant β-lactamase resistance gene, followed by blaCTX-M1 and blaOXA genes, which were detected in 21, 16, and 14 isolates respectively).

CONCLUSION

The high prevalence of MDR-, colistin-, cefepime-, and levofloxacin-resistant Salmonella serovars among Salmonella isolates from native chicken is alarming as these antimicrobials are critically important in treating severe salmonellosis cases and boost the urgent need for controlling antibiotic usage in veterinary and human medicine to protect public health.

Phylogenetic analysis of Staphylococcus aureus enterotoxin A gene in Iraqi breed cows with bovine mastitis: Implications for disease management

Background

Although milk is nutritionally valuable, it also serves as a significant medium for the transmission of pathogens and their toxins.

Aim

This study aimed to investigate the role of enterotoxin gene A (SEA) in the development of bovine mastitis. We accomplished this by examining milk through polymerase chain reaction (PCR) testing, amino acid substitution analysis, and phylogenetic analysis.

Methods

A total of fifty milk samples were collected from locally bred dairy cows in Al-Diwaniyah, located in southern Iraq. We employed the VITEK-2 platform to validate the diagnosis of Staphylococcus aureus and confirm the results of routine tests (culturing and biochemical tests). Subsequently, the genetic mutation and phylogeny analysis were achieved utilizing DNA sequencing to 16S rRNA and enterotoxin A genes.

Results

66% (33/50) of the milk samples found to be contain S. aureus by the VITEK-2 system. Furthermore, 25/33 of the samples were positive by the PCR test. While 60% (15 out of 25) tested positive for the SEA gene. After genomic analysis, we identified amino acid substitutions of serine, glutamine with arginine, tyrosine with cysteine, and aspartic acid with glycine at positions 9, 101, 119, 187, and 191. The phylogenetic investigation demonstrated a genetic relationship between our isolates (Iraqi isolates) and isolates from Indian and the United States.

Conclusion

Our study indicated the widespread distribution of the enterotoxin gene A (SEA) of S. aureus among dairy cows. The molecular study revealed significant changes in key amino acids that could play an important role in the bacterium's pathogenesis. The phylogenetic similarities among S. aureus samples from various countries suggest that the bacteria has spread globally.

High prevalence of multidrug-resistant Pseudomonas aeruginosa carrying integron and exoA, exoS, and exoU genes isolated from burn patients in Ahvaz, southwest Iran: A retrospective study

Background

Pseudomonas aeruginosa as an opportunistic pathogen produces several virulence factors. This study evaluated the relative frequency of exoenzymes (exo) A, U and S genes and integron classes (I, II, and III) among multi-drug-resistant clinical P. aeruginosa isolates from burn patients in Ahvaz, southwest of Iran.

Methods

In this cross-sectional study P. aeruginosa isolates were recovered from 355 wound samples. The antimicrobial susceptibility test was done by disk agar diffusion method on Muller-Hinton agar according to the Clinical and Laboratory Standards Institute. MDR isolates were defined if they showed simultaneous resistance to 3 antibiotics. Extensively drug-resistant was defined as nonsusceptibility to at least one agent in all but two or fewer antimicrobial categories. The presence of class I, II, and III integrons and virulence genes was determined using a PCR assay on extracted DNA.

Results

Overall, 145 clinical P. aeruginosa isolates were confirmed with biochemical and PCR tests. Overall, 35% (52/145) of the isolates were taken from males and 64% (93/145) from female hospitalized burn patients. The highest resistance rates of P. aeruginosa isolates to antibiotics were related to piperacillin 59% (n = 86/145) and piperacillin-tazobactam 57% (n = 83/145). A total of 100% of isolates were resistant to at least one antibiotic. MDR and XDR P. aeruginosa had a frequency of 60% and 29%, respectively. The prevalence of integron classes I, II, and III in P. aeruginosa was 60%, 7.58%, and 3.44%, respectively. IntI was more common in MDR and XDR P. aeruginosa isolates. In addition, 70(48%) of P. aeruginosa isolates did not harbor integron genes. Besides, exoA, exoS, and exoU in P. aeruginosa had a frequency of 55%, 55%, and 56%, respectively.

Conclusion

It was found that P. aeruginosa as a potent pathogen with strong virulence factors and high antibiotic resistance in the health community can cause refractory diseases in burn patients.

Unveiling the genetic architecture and transmission dynamics of a novel multidrug-resistant plasmid harboring blaNDM-5 in E. Coli ST167: implications for antibiotic resistance management

BACKGROUND

The emergence of multidrug-resistant (MDR) Escherichia coli strains poses significant challenges in clinical settings, particularly when these strains harbor New Delhi metallo-ß-lactamase (NDM) gene, which confer resistance to carbapenems, a critical class of last-resort antibiotics. This study investigates the genetic characteristics and implications of a novel blaNDM-5-carrying plasmid pNDM-5-0083 isolated from an E. coli strain GZ04-0083 from clinical specimen in Zhongshan, China.

RESULTS

Phenotypic and genotypic evaluations confirmed that the E. coli ST167 strain GZ04-0083 is a multidrug-resistant organism, showing resistance to diverse classes of antibiotics including ß-lactams, carbapenems, fluoroquinolones, aminoglycosides, and sulfonamides, while maintaining susceptibility to monobactams. Investigations involving S1 pulsed-field gel electrophoresis, Southern blot analysis, and conjugation experiments, alongside genomic sequencing, confirmed the presence of the blaNDM-5 gene within a 146-kb IncFIB plasmid pNDM-5-0083. This evidence underscores a significant risk for the horizontal transfer of resistance genes among bacterial populations. Detailed annotations of genetic elements-such as resistance genes, transposons, and insertion sequences-and comparative BLAST analyses with other blaNDM-5-carrying plasmids, revealed a unique architectural configuration in the pNDM-5-0083. The MDR region of this plasmid shares a conserved gene arrangement (repA-IS15DIV-blaNDM-5-bleMBL-IS91-suI2-aadA2-dfrA12) with three previously reported plasmids, indicating a potential for dynamic genetic recombination and evolution within the MDR region. Additionally, the integration of virulence factors, including the iro and sit gene clusters and enolase, into its genetic architecture poses further therapeutic challenges by enhancing the strain's pathogenicity through improved host tissue colonization, immune evasion, and increased infection severity.

CONCLUSIONS

The detailed identification and characterization of pNDM-5-0083 enhance our understanding of the mechanisms facilitating the spread of carbapenem resistance. This study illuminates the intricate interplay among various genetic elements within the novel blaNDM-5-carrying plasmid, which are crucial for the stability and mobility of resistance genes across bacterial populations. These insights highlight the urgent need for ongoing surveillance and the development of effective strategies to curb the proliferation of antibiotic resistance.

Genome analyses of colistin-resistant high-risk blaNDM-5 producing Klebsiella pneumoniae ST147 and Pseudomonas aeruginosa ST235 and ST357 in clinical settings

BACKGROUND

Colistin is a last-resort antibiotic used in extreme cases of multi-drug resistant (MDR) Gram-negative bacterial infections. Colistin resistance has increased in recent years and often goes undetected due to the inefficiency of predominantly used standard antibiotic susceptibility tests (AST). To address this challenge, we aimed to detect the prevalence of colistin resistance strains through both Vitek®2 and broth micro-dilution. We investigated 1748 blood, tracheal aspirate, and pleural fluid samples from the Intensive Care Unit (ICU), Neonatal Intensive Care Unit (NICU), and Tuberculosis and Respiratory Disease centre (TBRD) in an India hospital. Whole-genome sequencing (WGS) of extremely drug-resitant (XDR) and pan-drug resistant (PDR) strains revealed the resistance mechanisms through the Resistance Gene Identifier (RGI.v6.0.0) and Snippy.v4.6.0. Abricate.v1.0.1, PlasmidFinder.v2.1, MobileElementFinder.v1.0.3 etc. detected virulence factors, and mobile genetic elements associated to uncover the pathogenecity and the role of horizontal gene transfer (HGT).

RESULTS

This study reveals compelling insights into colistin resistance among global high-risk clinical isolates: Klebsiella pneumoniae ST147 (16/20), Pseudomonas aeruginosa ST235 (3/20), and ST357 (1/20). Vitek®2 found 6 colistin-resistant strains (minimum inhibitory concentrations, MIC = 4 μg/mL), while broth microdilution identified 48 (MIC = 32-128 μg/mL), adhering to CLSI guidelines. Despite the absence of mobile colistin resistance (mcr) genes, mechanisms underlying colistin resistance included mgrB deletion, phosphoethanolamine transferases arnT, eptB, ompA, and mutations in pmrB (T246A, R256G) and eptA (V50L, A135P, I138V, C27F) in K. pneumoniae. P. aeruginosa harbored phosphoethanolamine transferases basS/pmrb, basR, arnA, cprR, cprS, alongside pmrB (G362S), and parS (H398R) mutations. Both strains carried diverse clinically relevant antimicrobial resistance genes (ARGs), including plasmid-mediated blaNDM-5 (K. pneumoniae ST147) and chromosomally mediated blaNDM-1 (P. aeruginosa ST357).

CONCLUSION

The global surge in MDR, XDR and PDR bacteria necessitates last-resort antibiotics such as colistin. However, escalating resistance, particularly to colistin, presents a critical challenge. Inefficient colistin resistance detection methods, including Vitek2, alongside limited surveillance resources, accentuate the need for improved strategies. Whole-genome sequencing revealed alarming colistin resistance among K. pneumoniae and P. aeruginosa in an Indian hospital. The identification of XDR and PDR strains underscores urgency for enhanced surveillance and infection control. SNP analysis elucidated resistance mechanisms, highlighting the complexity of combatting resistance.

Virulent and Multi-drug-Resistant Edwardsiella tarda Infection in Oscar Fish: Unveiling the Threat of Mass Mortality and AMR Dissemination

The Oscar fish (Astronotus ocellatus) is among the most commonly domesticated and exported ornamental fish species from Kerala. The ornamental fish industry faces a significant challenge with the emergence of diseases caused by multi-drug-resistant bacteria. In the present study, six isolates were resolved from the diseased Oscar fish showing haemorrhages, necrosis, and loss of pigmentation. After phenotypic and genotypic characterization, the bacteria were identified as Edwardsiella tarda, Klebsiella pneumoniae, Enterococcus faecalis, Escherichia coli, Brevibacillus borstelensis, and Staphylococcus hominis. Experimental challenge studies in healthy Oscar fish showed that E. tarda caused 100% mortality within 240 h with 6.99 × 106 CFU/fish as LD50 and histopathology revealed the typical signs of infection. The pathogen was re-recovered from the moribund fish thereby confirming Koch's postulates. E. tarda was confirmed through the positive amplification of tarda-specific gene and virulence genes viz., etfD and escB were also detected using PCR. Antibiotic susceptibility tests using disc diffusion displayed that the pathogen is multi-drug-resistant towards antibiotics belonging to aminoglycosides, tetracyclines, and quinolones categories with a MAR index of 0.32, which implicated the antibiotic pressure in the farm. Plasmid curing studies showed a paradigm shift in the resistance pattern with MAR index of 0.04, highlighting the resistance genes are plasmid-borne except for the chromosome-borne tetracycline resistance gene (tetA). This study is the first of its kind in detecting mass mortality caused by E. tarda in Oscar fish. Vigilant surveillance and strategic actions are crucial for the precise detection of pathogens and AMR in aquaculture.

Proteome analysis, genetic characterization, and antibiotic resistance patterns of Klebsiella pneumoniae clinical isolates

Klebsiella pneumoniae (K. pneumoniae) is a member of the ESKAPE group and is responsible for severe community and healthcare-associated infections. Certain Klebsiella species have very similar phenotypes, which presents a challenge in identifying K. pneumoniae. Multidrug-resistant K. pneumoniae is also a serious global problem that needs to be addressed. A total of 190 isolates were isolated from urine (n = 69), respiratory (n = 52), wound (n = 48) and blood (n = 21) samples collected from various hospitals in the Al-Qassim, Saudi Arabia, between March 2021 and October 2022. Our study aimed to rapidly and accurately detect K. pneumoniae using the Peptide Mass Fingerprinting (PMF) technique, confirmed by real-time PCR. Additionally, screening for antibiotic susceptibility and resistance was conducted. The primary methods for identifying K. pneumoniae isolates were culture, Gram staining, and the Vitek® 2 ID Compact system. An automated MALDI Biotyper (MBT) instrument was used for proteome identification, which was subsequently confirmed using SYBR green real-time polymerase chain reaction (real-time PCR) and microfluidic electrophoresis assays. Vitek® 2 AST-GN66 cards were utilized to evaluate the antimicrobial sensitivity of K. pneumoniae isolates. According to our results, Vitek® 2 Compact accurately identified 178 out of 190 (93.68%) K. pneumoniae isolates, while the PMF technique correctly detected 188 out of 190 (98.95%) isolates with a score value of 2.00 or higher. Principal component analysis was conducted using MBT Compass software to classify K. pneumoniae isolates based on their structure. Based on the analysis of the single peak intensities generated by MBT, the highest peak values were found at 3444, 5022, 5525, 6847, and 7537 m/z. K. pneumoniae gene testing confirmed the PMF results, with 90.53% detecting entrobactin, 70% detecting 16 S rRNA, and 32.63% detecting ferric iron uptake. The resistance of the K. pneumoniae isolates to antibiotics was as follows: 64.75% for cefazolin, 62.63% for trimethoprim/sulfamethoxazole, 59.45% for ampicillin, 58.42% for cefoxitin, 57.37% for ceftriaxone, 53.68% for cefepime, 52.11% for ampicillin-sulbactam, 50.53% for ceftazidime, 52.11% for ertapenem, and 49.47% for imipenem. Based on the results of the double-disk synergy test, 93 out of 190 (48.95%) K. pneumoniae isolates were extended-spectrum beta-lactamase. In conclusion, PMF is a powerful analytical technique used to identify K. pneumoniae isolates from clinical samples based on their proteomic characteristics. K. pneumoniae isolates have shown increasing resistance to antibiotics from different classes, including carbapenem, which poses a significant threat to human health as these infections may become difficult to treat.

Unveiling the ocular battlefield: Insights into Pseudomonas aeruginosa virulence factors and their implications for multidrug resistance

The research investigates the virulence factors of Pseudomonas aeruginosa (P. aeruginosa), a pathogen known for its ability to cause human infections by releasing various exoenzymes and virulence factors. Particularly relevant in ocular infections, where tissue degeneration can occur, even after bacterial growth has ceased due to the potential role of secreted proteins/enzymes. Clinical isolates of P. aeruginosa, both ocular (146) and non-ocular (54), were examined to determine the frequency and mechanism of virulence factors. Phenotypic characterization revealed the production of alginate, biofilm, phospholipase C, and alkaline protease, while genotypic testing using internal uniplex PCR identified the presence of Exo U, S, T, Y, and LasB genes. Results showed a significant prevalence of Exo U and Y genes in ocular isolates, a finding unique to Indian studies. Additionally, the study noted that ocular isolates often contained all four secretomes, suggesting a potential link between these factors and ocular infections. These findings contribute to understanding the pathogenesis of P. aeruginosa infections, particularly in ocular contexts, and highlights the importance of comprehensive virulence factor analysis in clinical settings.

Phenotypic heterogeneity unveils a negative correlation between antibiotic resistance and quorum sensing in Pseudomonas aeruginosa clinical isolates

Colonization of Pseudomonas aeruginosa in the lung environments frequently leads to the enrichment of strains displaying enhanced antibiotic resistance and reduced production of quorum-sensing (QS) controlled products. However, the relationship between the emergence of QS deficient variants and antibiotic resistance remains less understood. In this study, 67 P. aeruginosa strains were isolated from the lungs of 14 patients with chronic obstructive pulmonary disease, followed by determining their genetic relationship, QS-related phenotypes and resistance to commonly used antibiotics. The integrity of P. aeruginosa QS system was checked by DNA sequencing. The relationship between the QS system and antibiotic resistance was then assessed by correlation analyses. The function of the LasR protein and bacterial virulence were evaluated through homology modeling and nematode-infection assay. The influence of antibiotic on the development of extracellular protease production ability of P. aeruginosa was tested by an evolutionary experiment. The results showed that P. aeruginosa clinical strains displayed abundant diversity in phenotype and genotype. The production of extracellular proteases was significantly negatively correlated with antibiotic resistance. The strains with enhanced antibiotic resistance also showed a notable overlap with the mutation of lasR gene, which is the core regulatory gene of P. aeruginosa QS system. Molecular docking and Caenorhabditis elegans infection assays further suggested that P. aeruginosa with impaired LasR protein could also have varying pathogenicity. Moreover, in vitro evolution experiments demonstrated that antibiotic-mediated selective pressure, particularly from Levofloxacin contributed to the emergence of extracellular protease-negative strains. Therefore, this study provides evidence for the connection of P. aeruginosa QS system and antibiotic resistance, and holds significance for developing targeted strategies to address antibiotic resistance and improving the management of antibiotic-resistant infections in chronic respiratory diseases.

Meat and meat products as potential sources of emerging MDR Bacillus cereus: groEL gene sequencing, toxigenic and antimicrobial resistance

BACKGROUND

Bacillus cereus is implicated in severe foodborne infection in humans. This study intended to assess the occurrence, groEL gene sequencing, biofilm production, and resistance profiles of emerged multidrug resistant (MDR) B. cereus in meat and meat product samples. Moreover, this work highlights the virulence and toxigenic genes (hblABCD complex, nheABC complex, cytK, ces, and pc-plc) and antimicrobial resistance genes (bla1, tetA, bla2, tetB, and ermA).

METHODS

Consequently, 200 samples (sausage, minced meat, luncheon, beef meat, and liver; n = 40 for each) were indiscriminately collected from commercial supermarkets in Port Said Province, Egypt, from March to May 2021. Subsequently, food samples were bacteriologically examined. The obtained isolates were tested for groEL gene sequence analysis, antibiotic susceptibility, biofilm production, and PCR screening of toxigenic and resistance genes.

RESULTS

The overall prevalence of B. cereus among the inspected food samples was 21%, where the highest predominance was detected in minced meat (42.5%), followed by beef meat (30%). The phylogenetic analysis of the groEL gene exposed that the examined B. cereus strain disclosed a notable genetic identity with other strains from the USA and China. Moreover, the obtained B. cereus strains revealed β-hemolytic activity, and 88.1% of the recovered strains tested positive for biofilm production. PCR evidenced that the obtained B. cereus strains usually inherited the nhe complex genes (nheA and nheC: 100%, and nheB: 83.3%), followed by cytK (76.2%), hbl complex (hblC and hblD: 59.5%, hblB: 16.6%, and hblA: 11.9%), ces (54.7%), and pc-plc (30.9%) virulence genes. Likewise, 42.9% of the examined B. cereus strains were MDR to six antimicrobial classes and encoded bla1, bla2, ermA, and tetA genes.

CONCLUSION

In summary, this study highlights the presence of MDR B. cereus in meat and meat products, posing a significant public health risk. The contamination by B. cereus is common in minced meat and beef meat. The molecular assay is a reliable fundamental tool for screening emerging MDR B. cereus strains in meat and meat products.

Characterisation of a Novel Tigecycline Resistance Gene tet(X22) and its Coexistence with blaNDM-1 in a Pseudomonas caeni Isolate

OBJECTIVES

The emergence of pathogens that are resistant to both tigecycline and carbapenem poses a threat to public health globally. Continuous emergence of novel tet(X) variants accelerates the tigecycline resistance crisis. This study aimed to characterise the novel tigecycline resistance gene tet(X22) and its coexistence with carbapenem resistance gene blaNDM-1 in Pseudomonas caeni.

METHODS

This P. caeni isolate co-harbouring tet(X22) and blaNDM-1 was systematically investigated using antimicrobial susceptibility testing, conjugation assays, genome sequencing, bioinformatic analyses, cloning of tet(X22) and functional analysis, and protein structure prediction.

RESULTS

The carbapenem-resistant and tigecycline-resistant P. caeni isolate CE14 was obtained from chicken faeces in 2022. CE14 carried multiple antibiotic resistance genes, including the novel tet(X22) and blaNDM-1. Tet(X22) exhibited 64.72-90.48% amino acid identity with other variants [Tet(X) to Tet(X21)]. Cloning of the gene tet(X22) and protein structure prediction revealed that Tet(X22) confers resistance to tetracyclines, including tigecycline. tet(X22) and blaNDM-1 were located in two multidrug-resistant regions of the chromosome.

CONCLUSIONS

The occurrence of the novel ISCR2-flanked tet(X22) in P. caeni suggests that the tet(X) variant has adapted to new hosts and may widely spread to further expand the host range. The future global spread of such pathogens co-harbouring tet(X) and blaNDM variants needs to be continuously monitored according to the One Health approach.

Agar Contact Method as a Valuable Tool to Identify Slaughter Hygiene Deficiencies along the Slaughter Process by Longitudinally Sampling Pig Skin Surfaces

Examinations of total viable counts (TVCs) and Salmonella spp. on the skin of individual pigs during the slaughter process are useful to identify abattoir-specific risk factors for (cross-)contamination. At seven process stages (lairage to before chilling), pigs were bacteriologically investigated by repeatedly sampling the same animals using the agar contact method. The mean TVC of all pigs increased significantly at the first three tested process stages (mean count, after delivery: 5.70 log cfu/cm2, after showering: 6.27 log cfu/cm2, after stunning: 6.48 log cfu/cm2). Significant mean TVC reductions occurred after scalding/dehairing (mean count: 3.71 log cfu/cm2), after singeing/flaming (2.70 log cfu/cm2), and after evisceration (2.44 log cfu/cm2) compared with the respective preceding process stages. At the end of the slaughter line and before chilling, the mean TVC was 2.33 log cfu/cm2, showing that the slaughter process reduced contamination significantly. The slaughter process effectively reduced even very high levels of incoming TVCs, since at the individual animal level, at the end of the slaughter process, there was no difference in the TVCs of animals with initially high and initially low TVCs. Additionally, 12 Salmonella spp. isolates were recovered from 12 different pigs, but only until the stage after scalding/dehairing. Overall, the agar contact method used is valuable for detecting hygiene deficiencies at slaughter, and is animal-equitable, practical, and suitable for use on live animals.

Carbapenem resistance in Enterobacterales from agricultural, environmental and clinical origins: South Africa in a global context

Carbapenem agents are regarded as last-resort antibiotics, however, bacterial resistance towards carbapenems has been reported in both clinical and agricultural settings worldwide. Carbapenem resistance, defined as the resistance of a bacteria towards one or more carbapenem drugs, can be mediated in either of, or a combination of, three mechanisms-although, the mechanism mediated through the production of carbapenemases (β-lactamases that are able to enzymatically degrade carbapenems) is of most significance. Of particular concern is the occurrence of carbapenemase producing Enterobacterales (CPE), with literature describing a dramatic increase in resistance globally. In South Africa, increases of carbapenemase activity occurring in Enterobacter species, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa have recently been reported. CPE can also be found in agricultural environments, as global studies have documented numerous instances of CPE presence in various animals such as pigs, cattle, seafood, horses and dogs. However, most reports of CPE occurrence in agricultural settings come from Northern America, Europe and some parts of Asia, where more extensive research has been conducted to understand the CPE phenomenon. In comparison to clinical data, there are limited studies investigating the spread of CPE in agricultural settings in Africa, highlighting the importance of monitoring CPE in livestock environments and the food chain. Further research is necessary to uncover the true extent of CPE dissemination in South Africa. This review will discuss the phenomenon of bacterial antibiotic resistance (ABR), the applications of the carbapenem drug and the occurrence of carbapenem resistance globally.

Prevalence, antibiotic resistance profile, MBLs encoding genes, and biofilm formation among clinical carbapenem-resistant Enterobacterales isolated from patients in Mohammed VI University Hospital Centre, Morocco

Enterobacterales are frequently a major cause of human infections. The emergence of carbapenem resistance as well as the biofilm formation complicate their management. In this regard, this study aimed to investigate the prevalence, antibiogram, carbapenemase genes, and biofilm production among Enterobacterales. For this purpose, 18 172 clinical specimens from hospitalized patients at Mohammed VI University Hospital were collected over two years (2018-2019). The bacteriological investigation was performed to isolate Enterobacterales. Subsequently, BD-Phoenix and MALDI-TOF-MS were used for bacterial identification. The production of ESBLs and carbapenemases was assessed using phenotypic tests and PCR. The biofilm formation was eventually carried out. Out of 195 carbapenem-resistant Enterobacterales strains, 190 were carbapenemase producers, and 74 Enterobacterales produced metallo-beta-lactamases (MBLs). The PCR results revealed that blaNDM was the most common carbapenemase gene, present in 62 cases, followed by the co-existence of blaNDM and blaOXA-48 in 12 cases. Klebsiella pneumoniae was the most frequently identified species among the 74 New Delhi metallo-β-lactamase (NDM) isolates and the XDR resistance phenotype was the most prevalent with 58.10%. Additionally, all 74 NDM-positive Enterobacterales were able to form biofilms, with 82.4% being strong producers. This study highlights the need for rapid detection of carbapenemase and biofilm production in our hospital to manage this health concern.

IncHI1 plasmids are epidemic vectors that mediate transmission of tet(X4) in Escherichia coli isolated from China

Introduction

This study aimed to investigate the genetic factors promoting widespread Q6 dissemination of tet(X4) between Escherichia coli and to characterize the genetic contexts of tet(X4).

Methods

We isolated E. coli from feces, water, soil and flies collected across a large-scale chicken farm in China in 2020. Antimicrobial susceptibility testing and PFGE typing were used to identify tigecycline resistance and assess clonal relationships among isolates. Plasmids present and genome sequences were analyzed by conjugation, S1 pulsed-field gel electrophoresis (PFGE), plasmid stability testing and whole-genome sequencing.

Results

A total of 204 tigecycline-resistant E. coli were isolated from 662 samples. Of these, we identified 165 tet(X4)-carrying E. coli and these strains exhibited a high degree of multidrug resistance. Based on the geographical location distribution of the sampled areas, number of samples in each area and isolation rate of tigecycline-resistant strains and tet(X4)-carrying isolates, 72 tet(X4)-positive isolates were selected for further investigation. Tigecycline resistance was shown to be mobile in 72 isolates and three types of tet(X4)-carrying plasmids were identified, they were IncHI1 (n = 67), IncX1 (n = 3) and pO111-like/IncFIA(HI1) (n = 2). The pO111-like/IncFIA(HI1) is a novel plasmid capable of transferring tet(X4). The transfer efficiency of IncHI1 plasmids was extremely high in most cases and IncHI1 plasmids were stable when transferred into common recipient strains. The genetic structures flanked by IS1, IS26 and ISCR2 containing tet(X4) were complex and varied in different plasmids.

Discussion

The widespread dissemination of tigecycline-resistant E. coli is a major threat to public health. This data suggests careful use of tetracycline on farms is important to limit spread of resistance to tigecycline. Multiple mobile elements carrying tet(X4) are in circulation with IncHI1 plasmids the dominant vector in this setting.

Susceptibility and Virulence of Enterobacteriaceae Isolated from Urinary Tract Infections in Benin

Enterobacteriaceae represent one of the main families of Gram-negative bacilli responsible for serious urinary tract infections (UTIs). The present study aimed to define the resistance profile and the virulence of Enterobacteriaceae strains isolated in urinary tract infections in Benin. A total of 390 urine samples were collected from patients with UTIs, and Enterobacteriaceae strains were isolated according to standard microbiology methods. The API 20E gallery was used for biochemical identification. All the isolated strains were subjected to antimicrobial susceptibility testing using the disc diffusion method. Extended-spectrum beta-lactamase (ESBL) production was investigated using a double-disc synergy test (DDST), and biofilm production was quantified using the microplate method. Multiplex PCR was used to detect uro-virulence genes, namely: PapG, IronB, Sfa, iucD, Hly, FocG, Sat, FyuA and Cnf, using commercially designed primers. More than 26% (103/390) of our samples were contaminated by Enterobacteriaceae strains at different levels. Thus, E. coli (31.07%, 32/103), Serratia marcescens (11.65%, 12/103), Klebsiella ornithinolytica (8.74%, 9/103), Serratia fonticola (7.77%, 8/103) and Enterobacter cloacae (6.80%, 7/103) were identified. Among the isolated strains, 39.81% (41/103) were biofilm-forming, while 5.83% (6/103) were ESBL-producing. Isolates were most resistant to erythromycin, cefixime, ceftriaxone and ampicillin (≥90%) followed by ciprofloxacin, gentamycin, doxycycline and levofloxacin (≥50%), and least resistant to imipenem (27.18%). In regard to virulence genes, Sfa was the most detected (28.15%), followed by IronB (22.23%), iucD (21.36%), Cnf (15.53%), PapG (9.71%), FocG (8.74%), Sat (6.79%), FyuA (5.82%) and Hyl (2.91%). These data may help improve the diagnosis of uropathogenic strains of Enterobacteriaceae, but also in designing effective strategies and measures for the prevention and management of severe, recurrent, or complicated urinary tract infections in Benin.

High variation across E. coli hybrid isolates identified in metabolism-related biological pathways co-expressed with virulent genes

Virulent genes present in Escherichia coli (E. coli) can cause significant human diseases. These enteropathogenic E. coli (EPEC) and enterotoxigenic E. coli (ETEC) isolates with virulent genes show different expression levels when grown under diverse laboratory conditions. In this research, we have performed differential gene expression analysis using publicly available RNA-seq data on three pathogenic E. coli hybrid isolates in an attempt to characterize the variation in gene interactions that are altered by the presence or absence of virulent factors within the genome. Almost 26.7% of the common genes across these strains were found to be differentially expressed. Out of the 88 differentially expressed genes with virulent factors identified from PATRIC, nine were common in all these strains. A combination of Weighted Gene Co-Expression Network Analysis and Gene Ontology Enrichment Analysis reveals significant differences in gene co-expression involving virulent genes common among the three investigated strains. The co-expression pattern is observed to be especially variable among biological pathways involving metabolism-related genes. This suggests a potential difference in resource allocation or energy generation across the three isolates based on genomic variation.

In-Vitro and In-Vivo Antibacterial Effects of Frankincense Oil and Its Interaction with Some Antibiotics against Multidrug-Resistant Pathogens

Frankincense (Boswellia sacra oleo gum resin) is reported to possess antimicrobial activity against several pathogens in-vitro. The antimicrobial effects of frankincense oil and its interaction with imipenem and gentamicin against methicillin-resistant Staphylococcus aureus (MRSA) and multidrug-resistant P. aeruginosa were determined through in-vitro methods and an in-vivo study using a rat pneumonia model. Frankincense oil was subjected to GC-MS analysis to determine the different volatile components. Antibacterial effects against MRSA and MDR-P. aeruginosa was evaluated and its MIC and MBC were determined. For the rat pneumonia model (in-vivo), oil was administered at a dose of 500 mg/kg and 1000 mg/kg followed by determination of CFU in lung tissue and histological studies. Frankincense oil did not show a very potent inhibitory effect against MRSA or MDR-P. aeruginosa; the oil did not affect the zone of inhibition or FIC when combined with imipenem or gentamicin indicating a lack of interaction between the oil and the antibiotics. Furthermore, there was no interaction between the antibiotics and the frankincense oil in the in-vivo model. The result of the study revealed that frankincense oil has a weak inhibitory effect against MRSA and MDR-P. aeruginosa, and it did not show any interaction with imipenem or gentamicin.