Computational analyses of drug resistance mutations in katG and emb complexes in Mycobacterium tuberculosis.

The number of antibiotic resistant pathogens is increasing rapidly, and with this comes a substantial socioeconomic cost that threatens much of the world. To alleviate this problem, we must use antibiotics in a more responsible and informed way, further our understanding of the molecular basis of drug resistance, and design new antibiotics. Here, we focus on a key drug-resistant pathogen, Mycobacterium tuberculosis, and computationally analyze trends in drug-resistant mutations in genes of the proteins embA, embB, embC, and katG, which play essential roles in the action of the first-line drugs ethambutol and isoniazid. We use docking to predict binding modes of isoniazid to katG that agree with suggested binding sites found in our laboratory using cryo-EM. Using mutant stability predictions, we recapitulate the idea that resistance occurs when katG's heme cofactor is destabilized rather than due to a decrease in affinity to isoniazid. Conversely, we have identified resistance mutations that affect the affinity of ethambutol more drastically than the affinity of the natural substrate of embB. With this, we illustrate that we can distinguish between the two types of drug resistance-cofactor destabilization and drug affinity reduction-suggesting potential uses in the prediction of novel drug-resistant mutations.

IMI-Type Carbapenemase-Producing Enterobacter cloacae Complex, France and Overseas Regions, 2012-2022.

We characterized a collection of IMI-like-producing Enterobacter spp. isolates (n = 112) in France. The main clone corresponded to IMI-1-producing sequence type 820 E. cloacae subspecies cloacae that was involved in an outbreak. Clinicians should be aware of potential antimicrobial resistance among these bacteria.

Auritidibacter ignavus, an Emerging Pathogen Associated with Chronic Ear Infections.

We describe detection of the previously rarely reported gram-positive bacterium Auritidibacter ignavus in 3 cases of chronic ear infections in Germany. In all 3 cases, the patients had refractory otorrhea. Although their additional symptoms varied, all patients had an ear canal stenosis and A. ignavus detected in microbiologic swab specimens. A correct identification of A. ignavus in the clinical microbiology laboratory is hampered by the inability to identify it by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Also, the bacterium might easily be overlooked because of its morphologic similarity to bacterial species of the resident skin flora. We conclude that a high index of suspicion is warranted to identify A. ignavus and that it should be particularly considered in patients with chronic external otitis who do not respond clinically to quinolone ear drop therapy.

Potential emergence of terbinafine resistance by squalene epoxidase gene mutations: An 18-month cohort study of onychomycosis patients in the United States.

BACKGROUND: There is a concerning rise in antifungal-resistant dermatophytosis globally, with resistance to terbinafine conferred by point mutations in the squalene epoxidase (SQLE) gene. OBJECTIVES: Report changes in the prevalence and profile of SQLE mutations in onychomycosis patients in the United States. METHODS: A longitudinal cohort study of toenail samples was collected from suspected onychomycosis patients over an 18-month period from 2022 to 2023. Samples were submitted from across the United States and subjected to multiplex real-time polymerase chain reactions for dermatophyte detection, with further screening of SQLE mutations at four known hotspots (393Leu, 397Phe, 415Phe and 440His). RESULTS: A total of 62,056 samples were submitted (mean age: 57.5 years; female: 60.4%). Dermatophytes were detected in 38.5% of samples, primarily Trichophyton rubrum complex (83.6%) and T. mentagrophytes complex (10.7%). A survey of SQLE mutations was carried out in 22,610 dermatophyte samples; there was a significant increase in the prevalence of SQLE mutations between the first quarter of 2022 and the second quarter of 2023 (29.0 to 61.9 per 1000 persons). The Phe397Leu substitution was the predominant mutation; Phe415Ser and His440Tyr have also emerged which were previously reported as minor mutations in skin samples. The temporal change in mutation rates can be primarily attributed to the Phe415Ser substitution. Samples from elderly patients (>70 years) are more likely to be infected with the T. mentagrophytes complex including strains harbouring the Phe415Ser substitution. CONCLUSION: The prevalence of SQLE mutations among onychomycosis patients with Trichophyton infections may be underestimated. Older individuals may have a higher risk.

Investigation of some changes and clonal relationship in enterococci isolates due to relocation of a hospital.

Objectives: To investigate the isolation rates, antimicrobial resistance rates, minimum inhibitory concentration values of antimicrobial agents, and clonal relationships of Enterococcus faecalis and Enterococcus faeciumdue to the relocation of a hospital to a newly constructed building. METHODS: The comparative, prospective study was conducted at adult general intensive care units of the Mus State Hospital, Mus, Turkey, in two phases; before the relocation from January 25 to December 1, 2014, and after the relocation from February 10 to May 24, 2015. Rectal swab samples were collected 72 hours post-hospitalisation. Identification of Enterococcus faecalis and Enterococcus faeciumisolates was determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and antimicrobial resistance with minimum inhibitory concentration values was detected with Vitek 2 system. The clonal relatedness among the strains was investigated by pulsed-field gel electrophoresis. Data was analysed using SPSS 23. RESULTS: Of the 69 patients, 37(53.62%) were related to pre-relocation phase; 20(54.1%) females and 17(45.9%) males with mean age 62.81±21.71 years. There were 32(46.37%) patients in the post-relocation phase; 13(40.6%) females and 19(59.4%) males with mean age 62.69±21.35 years (p>0.05). Of the 84 enterococci strains isolated, 51(60.7%) were Enterococcus faecium; 28(55%) before relocation and 23(45%) after relocation (p=0.77). The remaining 33(39.3%) isolates were Enterococcus faecalis; 16(48.5%) before relocation and 17(51.5%) after relocation (p=0.73). Multiple strains were located in 7(18.9%) patients before relocation and in 7(21.9%) after relocation. In 1(3.1%) patient after relocation, 2(8.7%) Enterococcus faecium isolates with different resistance and pulsed-field gel electrophoresis patterns were detected. There were no significant differences between the isolation and antibiotic resistance rates before and after relocation (p>0.05), and a clonal relation between the isolates was not detected (p>0.05). Decreased minimum inhibitory concentration values were noted for some antibiotics. CONCLUSIONS: Clonal relationship between the isolates and change in the rates of isolation and antimicrobial resistance of Enterococcus faecalis and Enterococcus faecium was not detected due to relocation. Minimum inhibitory concentration values could be used to reveal relocation-related changes in isolates obtained from patients hospitalised in intensive care units.

Antibiotic resistance in the microbiota of periodontitis patients: an update of current findings.

Systemic antibiotics are an effective adjunct in the treatment of periodontitis, but their judicious use is necessary as antimicrobial resistance is a growing global concern. This review aims to explore the current understanding and insight related to antibiotic resistance in the subgingival microbiota of periodontitis patients. A search of MEDLINE (PubMed) was carried out from 1 January 2012 to 25 November 2021 for studies related to antibiotic resistance in periodontitis patients. Of the 90 articles identified, 12 studies were selected for inclusion. A significant incidence of antibiotic resistant isolates was reported for Porphyromonas gingivalis, Prevotella intermedia, Prevotella denticola, Prevotella melaninogenica, Fusobacterium nucleatum, Tanerella forsythia, Aggretibacter actinomycetemcomitans, Streptococcus constellatus, Streptococcus intermedius, and Parvimonas micra, but resistance to specific antibiotics did not reach above 10% of isolates in most studies except for amoxicillin resistance in Aggretibacter actinomycetemcomitans. The highest frequency of resistance across all bacterial species was for amoxicillin, clindamycin, and metronidazole. However, resistance patterns were widely variable across geographical locations, and the high heterogeneity between antibiotic-resistant isolates across studies precludes any clinical recommendations from this study. Although antibiotic resistance has yet to reach critical levels in periodontitis patients, an emphasis on antibiotic stewardship interventions such as point-of-care diagnostics and education for key stakeholders is needed to curb a growing problem.

Isolation of Hafnia paralvei co-harbouring blaNDM-1 and blaVIM-1 in a woman who underwent allogeneic hematopoietic stem cell transplantation.

Metallo-ß-lactamases (MBL) are a threat to public health, since they dramatically limit the use of ß-lactams. We report the isolation of a multidrug-resistant Hafnia paralvei strain from urine and a rectal swab of a female patient after allogeneic hematopoietic stem cell transplantation for myelodysplastic syndrome. Antimicrobial susceptibility testing yielded resistance to trimethoprim/sulfamethoxazole, colistin, fosfomycin and all ß-lactams, except cefiderocol. Whole genome sequencing revealed the presence of plasmid-encoded NDM-1 and VIM-1 carbapenemases. This finding highlights the importance of epidemiological surveillance and new therapeutic options for MBL.

Antimicrobial resistance and epidemic clustering of late-onset neonatal infections in a Brazilian intensive care unit.

Nosocomial infections in the neonatal intensive care unit (NICU) tend to cluster and multidrug-resistant (MDR) pathogens are rising in developing countries. We did a retrospective cohort study of neonates admitted to a NICU in Brazil with late-onset neonatal sepsis (LOS) confirmed by blood culture from October 2012 to December 2016 and from July 2018 to December 2021. We defined a cluster of infection when at least two cases of LOS occurred within two different time intervals: 15 and 30 days with the same pathogen in different patients. A random amplified polymorphic DNA (RAPD) was performed from samples from one of these clusters. A logistic regression model was applied having death as the outcome and the infection with an MDR pathogen as the exposure of interest. There were 987 blood cultures from 754 neonates, 621 (63%) were gram-positive cocci, 264 (30%) were gram-negative rods and 72 (7%) fungi. A third of Enterobacterales were resistant to cefepime and a third of non-fermenting glucose rods were resistant to carbapenems. There were 100 or 104 clusters of infection in the 15- or 30-day interval, respectively. A RAPD analysis from an outbreak of MDR Acinetobacter baumannii showed that all five samples belonged to a single clone. An infection with an MDR pathogen was associated with death (OR 1.82, 95% CI 1.03-3.21). In conclusion, clusters of infections in a Brazilian NICU are a frequent phenomenon as seen elsewhere. They suggest cross-transmission of pathogens with increasing antimicrobial resistance and should prompt intensified surveillance and infection control measures.

Association between bacterial resistance profile and the development of intra-abdominal abscesses in pediatric patients with perforated appendicitis: cohort study.

PURPOSE: The objective of this study was to determine the association between the presence of a microorganism resistant to the antibiotic used in empirical therapy and the development of intra-abdominal abscesses in children with perforated appendicitis. METHODS: A prospective cohort study was conducted in patients under 18 years of age who underwent laparoscopic appendectomy between November 1, 2019, and September 30, 2020, in whom perforated appendicitis was documented intraoperatively. Peritoneal fluid samples were taken for bacteria culture purposes, and clinical and microbiological data were collected from all patients. RESULTS: A total of 232 patients were included in the study. The most isolated microorganisms were Escherichia coli (80.14%) and Pseudomonas aeruginosa (7.45%). In addition, 5.31% of E. coli isolates were classified as ESBL-producing organisms. No association was found between a germ resistant to empiric antimicrobial therapy and the development of a postoperative intra-abdominal abscess. Multivariate analysis showed that being a high-risk patient on admission (OR 2.89 (p = 0.01)) was associated with the development of intra-abdominal abscesses postoperatively. CONCLUSION: E. coli was the most commonly isolated microorganism, with a low rate of ESBL-producing isolates. No association between resistance and risk of postoperative intra-abdominal abscess was found. However, it was identified that being a high-risk patient on admission was associated with this complication. TYPE OF STUDY: Prognosis study. LEVEL OF EVIDENCE: Level I.

Genomic and clinical case characterisation of Staphylococcus haemolyticus isolated from dogs and cats in the United States, including strains with high-level mupirocin tolerance.

BACKGROUND: Staphylococcus haemolyticus is a coagulase-negative commensal organism of both people and companion animals. It has pathogenic potential and when cultured is often meticillin- and multidrug-resistant. OBJECTIVES: To characterise the clinical features of dogs and cats with clinical skin disease that had positive S. haemolyticus skin cultures, and to employ whole-genome sequencing (WGS) to identify resistance genes and characterise the genetic relatedness of strains. MATERIALS AND METHODS: Isolates were identified by the institutional clinical microbiology laboratory by routine aerobic culture and susceptibility from seven veterinary hospitals across the United States. Then, WGS and analysis of each isolate were performed and clinical data collected via a retrospective clinician questionnaire. RESULTS: S. haemolyticus was identified from superficial (seven of 12) and deep (five of 12) cutaneous infections in our study. Most animals had received antimicrobials (10 of 12) and/or immunomodulatory drugs (nine of 12) within the six months before culture. WGS analysis revealed a variety of genetic lineages and a wide array of antimicrobial resistance genes. Meticillin resistance was identified in nine of 12 isolates and four of 12 isolates demonstrated mupirocin tolerance. CONCLUSIONS AND CLINICAL RELEVANCE: Staphylococcus haemolyticus may be an under-recognised pathogen in companion animals, and its demonstrated potential for multidrug-resistance, meticillin-resistance, and high-level mupirocin tolerance may create a therapeutic challenge. Further studies should evaluate the prior antimicrobial use and immunocompromised status as risk factors for infection with S. haemolyticus.

KNOWLEDGE OF ANTIMICROBIAL DRUG RESISTANCE (AMR) AMONG PATIENTS IN A GENERAL OUTPATIENT CLINIC IN ABUJA MUNICIPAL AREA COUNCIL (AMAC), FEDERAL CAPITAL TERRITORY, NIGERIA.

Introduction: Antimicrobial resistance (AMR) is currently prevalent and has the potential to affect everyone, of any age, in any country. In humans, animals, and the environment, antimicrobial-resistant microbes are quickly emerging and spreading. This study aims to assess the knowledge of Antimicrobial Drug Resistance (AMR) among patients in a General Outpatient Clinic in Abuja Municipal Area Council (AMAC), Federal Capital Territory, Nigeria. Methodology: This was a descriptive cross-sectional study among 400 clients in a district hospital done in 2022 using a multistage sampling technique. Data was collected using a self-administered structured questionnaire and analyzed and presented as tables, proportions, and percentages using the IBM SPSS 28 Statistical Package for the Social Sciences. Ethical approval was granted by Bingham University Teaching Hospital Ethical Research Committee, Jos, and Plateau State. Results: The study revealed that 8.5% of female respondents had good knowledge, 20.75% had fair knowledge while 27.75% had poor knowledge. Of all the male respondents, 8.5% had good knowledge, 13% had fair knowledge and 21.5% had poor knowledge. Summarily, only 68 (17.0%) of participants had good knowledge of antimicrobial resistance, 135 (33.75%) had fair knowledge of antimicrobial resistance, and 197 (49.25%) had poor knowledge of antimicrobial resistance. Test of association between knowledge of antimicrobial resistance and socio-demographics showed that marital status (χ² = 44.28, p < 0.045), Education (χ²= 123.80, p < 0.001), and Age (χ² = 112.95, p < 0.001) were statistically significant. Conclusion: The Federal, State, and Local governments, health care providers, and community health workers should focus on increasing awareness of AMR risk factors through health campaigns and programs that will aid behavioral change.

Increasing Antimicrobial Resistance in World Health Organization Eastern Mediterranean Region, 2017-2019.

To better guide the regional response to antimicrobial resistance (AMR), we report the burden of AMR over time in countries in the World Health Organization Eastern Mediterranean Region. To assess the capacities of national infection prevention and control and antimicrobial stewardship programs, we analyzed data on bloodstream infections reported to the Global Antimicrobial Resistance Surveillance System during 2017-2019, data from 7 countries on nationally representative surveys of antimicrobial prescriptions, and data from 2 regional surveys. The median proportion of bloodstream infections was highest for carbapenem-resistant Acinetobacter spp. (70.3%) and lowest for carbapenem-resistant Escherichia coli (4.6%). Results of the regional assessments indicate that few countries have capacities for infection prevention and control and antimicrobial stewardship programs to prevent emergence and spread of AMR. Overall, the magnitude of the problem and the limited capacity to respond emphasize the need for regional political leadership in addressing AMR.

RamAp Is an Efflux Pump Regulator Carried by an IncHI2 Plasmid.

In investigating the epidemiological trends of Salmonella enterica serovar Goldcoast, we previously identified several closely related strains with different MICs to azithromycin and quinolones. Genome sequencing and comparison of two very similar multidrug-resistant (MDR) strains, R18.0877 and R18.1656, has led to the identification of an extra plasmid-borne ramA gene, ramAp, on the large IncHI2 plasmid carried by R18.0877. The ramAp gene is located in a 953-bp region on the plasmid, which is identical to that of the Klebsiella quasipneumoniae chromosomal ramA loci. A truncated ISEcp1 located at the adjacent upstream area of the putative regulatory region of ramAp may likely contribute to its mobilization and expression. Introducing the ramAp gene and the truncated ISEcp1 into Escherichia coli has resulted in elevated expression of efflux pump genes and elevated MICs to chloramphenicol, azithromycin, nalidixic acid, ciprofloxacin, sulfamethoxazole, trimethoprim, tetracycline, and tigecycline. The ramAp is an extra efflux pump activator gene that potentially could be transmitted with the IncHI2 plasmid among bacteria. It is plausible that, with high interspecific conservation, the plasmid-encoded regulator reduces drug susceptibility by activating existing efflux pump systems of the host and thus can be regarded as a new type of auxiliary antimicrobial resistance determinant. Sequences of similar plasmids were found worldwide. Its impact on the emergence of antimicrobial resistance among bacterial pathogens is worrisome.

Phenotypic and genotypic changes of Staphylococcus aureus in the presence of the inappropriate concentration of chlorhexidine gluconate.

BACKGROUND: Chlorhexidine gluconate (CHG) is a disinfectant agent with different applications in health care. Improper use of CHG causes antimicrobial resistance in bacteria as a public health threat. Since Staphylococcus aureus is a common bacteria, it is expected usually exposed to CHG in the hospital and community. The present study aimed to correlate the phenotypic and genotypic changes in a S. aureus strain upon serial adaptation with supra-inhibitory CHG concentration for 50 days. RESULTS: After in vitro serial culture of 5 × 105 CFU/ml of a clinical vancomycin-susceptible S. aureus strain (VAN-S) into brain heart infusion (BHI) broth containing CHG 1/4, 1/2, 1, and 2 × minimal inhibitory concentration (MIC) values of VAN-S in 37 °C during 50 days, we isolated a S. aureus strain (CHGVan-I) with a ≥ twofold decrease in susceptibility to CHG and vancomycin. CHG-induced CHGVan-I strain was considered as a vancomycin-intermediate S. aureus (VISA) strain with a VAN MIC of 4 µg/ml using the broth macro dilution method. However, reduced resistance was observed to tetracycline family antibiotics (doxycycline and tetracycline) using a modified Kirby-Bauer disk diffusion test. Moreover, a remarkable reduction was detected in growth rate, hemolysis activity (the lysis of human red blood cells by alpha-hemolysin), and colony pigmentation (on BHI agar plates). Biofilm formation (using the Microtiter plate method and crystal violet staining) was significantly increased upon CHG treatment. Adaptive changes in the expression of a set of common genes related to the development of VISA phenotype (graTSR, vraTSR, walKR, agr RNAIII, sceD, pbpB, and fmtA) were analyzed by Reverse Transcription quantitative PCR (RT-qPCR) experiment. Significant changes in vraTSR, agr RNAIII, sceD, and pbpB expression were observed. However, gene sequencing of the two-component system vraTSR using the Sanger sequencing method did not detect any non-synonymous substitution in CHGVan-I compared to wild-type. The clonality of VAN-S and CHGVan-I strains was verified using the pulsed-field gel electrophoresis (PFGE) method. CONCLUSIONS: The importance of the present study should be stated in new detected mechanisms underlying VISA development. We found a link between the improper CHX use and the development of phenotypic and genotypic features, typical of VISA clinical isolates, in a CHG-induced strain. Since disruption of the cell wall biosynthesis occurs in VISA isolates, our CHG-induced VISA strain proved new insights into the role of CHG in the stimulation of the S. aureus cell wall.

Effect of ciprofloxacin and in vitro gut conditions on biofilm of Escherichia coli isolated from clinical and environmental sources.

AIM: This study aimed at characterizing the biofilm-forming ability of drug-resistant and sensitive Escherichia coli under in vitro gut conditions and in the presence of ciprofloxacin. METHODS AND RESULTS: 153 E. coli isolates comprising 80 from clinical and 73 from environment source were studied for their ability to form biofilm under control and in vitro simulated gut conditions. The integrity of preformed biofilm on exposure to ciprofloxacin was assessed. Expression of biofilm-associated genes was analysed using qPCR. A high degree of resistance was observed in clinical isolates with a concomitant prevalence of blaTEM . Bile, pH and low temperature enabled the E. coli biofilm to resist the effect of ciprofloxacin. Clinical isolates of E. coli formed strong biofilms in in vitro gut conditions following exposure to high concentration of ciprofloxacin. The expression of biofilm genes varied between different gut conditions viz., presence of bile, pH and low temperature, included in this study. CONCLUSIONS: This study demonstrates the importance of papC and csgA for maintaining the biofilm integrity upon antibiotic exposure. Escherichia coli form biofilm as a survival strategy to adapt to the conditions in their environment irrespective of their drug resistance status. SIGNIFICANCE AND IMPACT OF THE STUDY: The study provides an understanding of the effect of different parameters of the gut conditions during infection and the effect of antibiotic on survival and biofilm-forming ability of clinical and environmental E. coli isolates. It further suggests that bacteria resort to biofilm formation as one of the mechanisms to adjust to alterations in gut conditions and once the biofilm is formed, it requires high concentration of ciprofloxacin to eradicate it.

Level of biofilm production by Staphylococcus aureus isolates is critical for resistance against most but not all antimicrobial drugs.

Background and Objective: Staphylococcal biofilms cause a wide range of acute and chronic infections, both in hospital and community settings across the world. This study explores biofilm forming propensity among Staphylococcus aureus clinical isolates from Faisalabad, Pakistan and their association with antimicrobial drug resistance. Methods: The study was conducted during July to December 2020. The biofilm forming ability of S. aureus isolates was assessed by crystal violet staining in 96 well plates. Antimicrobial susceptibility was determined by disk diffusion method against ten antimicrobials representing whole spectrum of antimicrobial drugs. Results: All the isolates (n=22) produced biofilm; 14 (63.6%) were strong, and 8 (36.4%) moderate biofilm producers. Comparative data were obtained for moderate and strong biofilm producers. Increased biofilm production did not affect azithromycin, clindamycin and mupirocin. However, stronger biofilm production significantly increased resistant isolates in case of augmentin (23.2%), cefoxitin (17.9%), levofloxacin (26.8%), tetracycline (23.2%), vancomycin (14.3%) and trimethoprim (21.4%). Conclusions: Our findings indicate that the ability to produce large amount of biofilm is an important factor, and S. aureus isolates with this ability, do not require acquisition of drug resistance genes from other bacteria. Our study also provides a guideline for selection of antimicrobials which are not adversely affected by level of biofilm production by various strains of S. aureus.

Pseudomonas aeruginosa Susceptibility Patterns and Associated Clinical Outcomes in People with Cystic Fibrosis following Approval of Aztreonam Lysine for Inhalation.

The approval of aztreonam lysine for inhalation solution (AZLI) raised concerns that additional antibiotic exposure would potentially affect the susceptibility profiles of Pseudomonas aeruginosa isolates from cystic fibrosis (CF) patients. This 5-year, prospective, observational study tracked susceptibility changes and clinical outcomes in CF patients in the United States with chronic P. aeruginosa infection. Sputum cultures were collected annually (2011 to 2016). The primary study endpoint was the proportion of subjects whose least susceptible P. aeruginosa isolate had an aztreonam MIC that was >8 µg/ml (parenteral breakpoint) and increased ≥4-fold compared with the least susceptible isolate from the previous year. Annualized data for pulmonary exacerbations, hospitalizations, and percent of predicted forced expiratory volume in 1 s (FEV1% predicted) were obtained from the CF Foundation Patient Registry and compared between subjects meeting and those not meeting the primary endpoint. A total of 510 subjects were enrolled; 334 (65%) completed the study. A consistent proportion of evaluable subjects (13 to 22%) met the primary endpoint each year, and AZLI use during the previous 12 months was not associated with meeting the primary endpoint. While the annual declines in lung function were comparable for subjects meeting and those not meeting the primary endpoint, more pulmonary exacerbations and hospitalizations were experienced by those who met it. The aztreonam susceptibility of P. aeruginosa remained consistent during the 5-year study. The relationship between P. aeruginosa isolate susceptibilities and clinical outcomes is complex; reduced susceptibility was not associated with an accelerated decline in lung function but was associated with more exacerbations and hospitalizations, likely reflecting increased overall antibiotic exposure. (This study has been registered at ClinicalTrials.gov under identifier NCT01375036.).

Investigating the effect of an identified mutation within a critical site of PAS domain of WalK protein in a vancomycin-intermediate resistant Staphylococcus aureus by computational approaches.

BACKGROUND: Vancomycin-intermediate resistant Staphylococcus aureus (VISA) is becoming a common cause of nosocomial infections worldwide. VISA isolates are developed by unclear molecular mechanisms via mutations in several genes, including walKR. Although studies have verified some of these mutations, there are a few studies that pay attention to the importance of molecular modelling of mutations. METHOD: For genomic and transcriptomic comparisons in a laboratory-derived VISA strain and its parental strain, Sanger sequencing and reverse transcriptase quantitative PCR (RT-qPCR) methods were used, respectively. After structural protein mapping of the detected mutation, mutation effects were analyzed using molecular computational approaches and crystal structures of related proteins. RESULTS: A mutation WalK-H364R was occurred in a functional zinc ion coordinating residue within the PAS domain in the VISA strain. WalK-H364R was predicted to destabilize protein and decrease WalK interactions with proteins and nucleic acids. The RT-qPCR method showed downregulation of walKR, WalKR-regulated autolysins, and agr locus. CONCLUSION: Overall, WalK-H364R mutation within a critical metal-coordinating site was presumably related to the VISA development. We assume that the WalK-H364R mutation resulted in deleterious effects on protein, which was verified by walKR gene expression changes.. Therefore, molecular modelling provides detailed insight into the molecular mechanism of VISA development, in particular, where allelic replacement experiments are not readily available.

Clostridioides difficile in COVID-19 Patients, Detroit, Michigan, USA, March-April 2020.

We describe 9 patients at a medical center in Detroit, Michigan, USA, with severe acute respiratory syndrome coronavirus 2 and Clostridioides difficile. Both infections can manifest as digestive symptoms and merit screening when assessing patients with diarrhea during the coronavirus disease pandemic. These co-infections also highlight the continued importance of antimicrobial stewardship.

Drug-resistant enteric fever worldwide, 1990 to 2018: a systematic review and meta-analysis.

BACKGROUND: Antimicrobial resistance (AMR) is an increasing threat to global health. There are > 14 million cases of enteric fever every year and > 135,000 deaths. The disease is primarily controlled by antimicrobial treatment, but this is becoming increasingly difficult due to AMR. Our objectives were to assess the prevalence and geographic distribution of AMR in Salmonella enterica serovars Typhi and Paratyphi A infections globally, to evaluate the extent of the problem, and to facilitate the creation of geospatial maps of AMR prevalence to help targeted public health intervention. METHODS: We performed a systematic review of the literature by searching seven databases for studies published between 1990 and 2018. We recategorised isolates to allow the analysis of fluoroquinolone resistance trends over the study period. The prevalence of multidrug resistance (MDR) and fluoroquinolone non-susceptibility (FQNS) in individual studies was illustrated by forest plots, and a random effects meta-analysis was performed, stratified by Global Burden of Disease (GBD) region and 5-year time period. Heterogeneity was assessed using the I2 statistics. We present a descriptive analysis of ceftriaxone and azithromycin resistance. FINDINGS: We identified 4557 articles, of which 384, comprising 124,347 isolates (94,616 S. Typhi and 29,731 S. Paratyphi A) met the pre-specified inclusion criteria. The majority (276/384; 72%) of studies were from South Asia; 40 (10%) articles were identified from Sub-Saharan Africa. With the exception of MDR S. Typhi in South Asia, which declined between 1990 and 2018, and MDR S. Paratyphi A, which remained at low levels, resistance trends worsened for all antimicrobials in all regions. We identified several data gaps in Africa and the Middle East. Incomplete reporting of antimicrobial susceptibility testing (AST) and lack of quality assurance were identified. INTERPRETATION: Drug-resistant enteric fever is widespread in low- and middle-income countries, and the situation is worsening. It is essential that public health and clinical measures, which include improvements in water quality and sanitation, the deployment of S. Typhi vaccination, and an informed choice of treatment are implemented. However, there is no licenced vaccine for S. Paratyphi A. The standardised reporting of AST data and rollout of external quality control assessment are urgently needed to facilitate evidence-based policy and practice. TRIAL REGISTRATION: PROSPERO CRD42018029432.