Co-trimoxazole Resistance Research Articles

Antimicrobial Resistance of Environmental V. cholerae Non-O1/O139 Isolates: Systematic Review and Meta-analysis.

The understanding of the antibiotic resistance status of environmental nonO1/nonO139 V. cholerae [NOVC] in relation to other illnesses, which can vary in severity from mild to life-threatening, is limited. However, it is important to note that NOVC-related infections are increasing and serve as a significant illustration of emerging human diseases associated with climate change. The primary objective of the present study was to assess the rates of resistance observed in environmental NOVC isolates across various years, and regions, and their resistance rates. We performed a systematic search of Scopus, PubMed, Web of Science, and EMBASE databases [until May 2024] following PRISMA guidelines. All statistical analyses were carried out using the statistical package R. Our analysis included a total of 34 studies. According to the meta-regression, chlo-ramphenicol, rifampicin, ciprofloxacin, nalidixic acid, cotrimoxazole, kanamycin, trime-thoprim, amoxicillin/clavulanic acid, and tetracycline resistance rate increased over time. The lowest resistance rates were observed in Austria [amoxicillin; 0.6%], the United States [kana-mycin; 0.1% and tetracycline; 0.1%], Morocco [polymyxin B; 12%], and Spain [trimethoprim; 0.3%]. Conversely, the highest resistance rates were found in Spain [amoxicillin; 61%], Indo-nesia [kanamycin and tetracycline; 94.9%], India [polymyxin B; 97.8%], and Morocco [trime-thoprim; 48.9%]. The meta-analysis showed significant variability in antibiotic resistance patterns among environmental NOVC isolates across time and regions, emphasizing the need for tar-geted, time-specific, and country-specific approaches to address antibiotic resistance globally.

Prevalence of co-trimoxazole resistance among HIV-infected individuals in Ethiopia: a systematic review and meta-analysis.

Co-trimoxazole is used as a prophylaxis for human immunodeficiency virus (HIV) patients to prevent opportunistic infections. Its widespread use results in the emergence of co-trimoxazole resistance, which is a significant problem. This systematic review and meta-analysis determined the pooled prevalence of co-trimoxazole resistance among HIV-infected individuals in Ethiopia. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline was applied to report this study. The protocol has been registered in the International Prospective Register of Systematic Reviews (PROSPERO) under the assigned number CRD42024532240. Article search was performed using electronic databases such as PubMed, Medline, EMBASE, Google Scholar, Hinari, Web of Science, Science Direct, and African Journals Online. Data were extracted using a Microsoft Excel spreadsheet and analyzed using STATA version 11.0 software. A random-effects model was used to estimate the pooled effect size of co-trimoxazole resistance across studies with a 95% confidence interval. The heterogeneity was checked using I2 statistic. The presence of publication bias was determined using a funnel plot and Egger's test with a p-value <0.05 evidence of statistically significant bias. Subgroup and sensitivity analyses were performed. Twenty-two studies with 5,788 HIV-infected individuals were included. The pooled prevalence of co-trimoxazole resistance was 61.73% (95% CI: 53.10-70.37%), with heterogeneity (I2 = 87.7%) and statistical significance (p < 0.001). A higher co-trimoxazole resistance was observed in HIV-infected individuals with urinary tract infection; 82.10% (95% CI: 75.03-89.17%). Among the bacterial spp., higher resistance to co-trimoxazole was observed in Escherichia coli; 70.86% (95% CI: 53.44-88.27%) followed by Salmonella spp.; 67.66% (95% CI: 41.51-93.81%) and Proteus spp.; 66.23% (95% CI: 34.65-97.82%). There is a higher prevalence of co-trimoxazole resistance in HIV-infected individuals in Ethiopia. This alarms WHO's recommendation of co-trimoxazole prophylaxis guidelines to review and update it. Additionally, a nationwide assessment of co-trimoxazole resistance in Ethiopia as a whole is required.Systematic review registration: identifier: CRD42024532240.

Genetics of resistance to trimethoprim in cotrimoxazole resistant uropathogenic Escherichia coli: integrons, transposons, and single gene cassettes.

Cotrimoxazole, the combined formulation of sulfamethoxazole and trimethoprim, is one of the treatments of choice for several infectious diseases, particularly urinary tract infections. Both components of cotrimoxazole are synthetic antimicrobial drugs, and their combination was introduced into medical therapeutics about half a century ago. In Gram-negative bacteria, resistance to cotrimoxazole is widespread, being based on the acquisition of genes from the auxiliary genome that confer resistance to each of its antibacterial components. Starting from previous knowledge on the genotype of resistance to sulfamethoxazole in a collection of cotrimoxazole resistant uropathogenic Escherichia coli strains, this work focused on the identification of the genetic bases of the trimethoprim resistance of these same strains. Molecular techniques employed included PCR and Sanger sequencing of specific amplicons, conjugation experiments and NGS sequencing of the transferred plasmids. Mobile genetic elements conferring the trimethoprim resistance phenotype were identified and included integrons, transposons and single gene cassettes. Therefore, strains exhibited several ways to jointly resist both antibiotics, implying different levels of genetic linkage between genes conferring resistance to sulfamethoxazole (sul) and trimethoprim (dfrA). Two structures were particularly interesting because they represented a highly cohesive arrangements ensuring cotrimoxazole resistance. They both carried a single gene cassette, dfrA14 or dfrA1, integrated in two different points of a conserved cluster sul2-strA-strB, carried on transferable plasmids. The results suggest that the pressure exerted by cotrimoxazole on bacteria of our environment is still promoting the evolution toward increasingly compact gene arrangements, carried by mobile genetic elements that move them in the genome and also transfer them horizontally among bacteria.

Pneumococcal population genomics changes during the early time period of conjugate vaccine uptake in southern India.

Streptococcus pneumoniae is a major cause of invasive disease of young children in low- and middle-income countries. In southern India, pneumococcal conjugate vaccines (PCVs) that can prevent invasive pneumococcal disease began to be used more frequently after 2015. To characterize pneumococcal evolution during the early time period of PCV uptake in southern India, genomes were sequenced and selected characteristics were determined for 402 invasive isolates collected from children <5 years of age during routine surveillance from 1991 to 2020. Overall, the prevalence and diversity of vaccine type (VT) and non-vaccine type (NVT) isolates did not significantly change post-uptake of PCV. Individually, serotype 1 and global pneumococcal sequence cluster (GPSC or strain lineage) 2 significantly decreased, whereas serotypes 6B, 9V and 19A and GPSCs 1, 6, 10 and 23 significantly increased in proportion post-uptake of PCV. Resistance determinants to penicillin, erythromycin, co-trimoxazole, fluoroquinolones and tetracycline, and multidrug resistance significantly increased in proportion post-uptake of PCV and especially among VT isolates. Co-trimoxazole resistance determinants were common pre- and post-uptake of PCV (85 and 93 %, respectively) and experienced the highest rates of recombination in the genome. Accessory gene frequencies were seen to be changing by small amounts across the frequency spectrum specifically among VT isolates, with the largest changes linked to antimicrobial resistance determinants. In summary, these results indicate that as of 2020 this pneumococcal population was not yet approaching a PCV-induced equilibrium and they highlight changes related to antimicrobial resistance. Augmenting PCV coverage and prudent use of antimicrobials are needed to counter invasive pneumococcal disease in this region.

Antimicrobial resistance of E. coli strains in ready-to-eat red meat products in Nakuru County, Kenya

The demand for Ready-To-Eat (RTE) meat products is rising especially to the busy urban dwellers. Handling, processing, and selling methods of RTE contaminate them with pathogens. However, there is lack of evidence of the risk of antimicrobial resistance (AMR) of the pathogens. In this study, 105 RTE meat products were sampled across Nakuru County and assessed for Escherichia coli load, antimicrobial resistance (AMR), and presence of AMR genes. All the sampled meat products were contaminated with coliforms and E. coli but levels differed significantly (p < 0.05) with location of sample collection and type of RTE. Antimicrobial susceptibility test results of 30 E. coli isolates indicated high prevalence of the isolates’ resistance to co-trimoxazole, tetracycline, streptomycin, and ampicillin at 80%, 73%, 67%, and 67%, respectively. Antibiotic susceptibility of the isolates was highest towards ciprofloxacin and amikacin at 100% and 80%, respectively. All the 30 E. coli isolates showed 14 different AMR patterns, where each isolate was resistant to at least 2 antibiotics; a multiple antibiotic resistance (MAR) index of greater than 0.2. Meat samples collected from one sampling location, Salgaa had the highest number of multi-drug resistant E. coli isolates (88.9%). Molecular identification of AMR genes in four MAR isolates showed that tetA (for tetracycline resistance) and sul1 (for co-trimoxazole resistance) genes were present in all (100.0%) the isolates, while blaTEM (for ampicillin resistance) and strA (for streptomycin) genes were both present in two isolates. The four isolates were not E. coli O157 as confirmed by PCR for the O157 lipopolysaccharide O-antigen synthesis gene rfbE-O157. This study demonstrated the presence of MAR E. coli in RTE red meat products sold in Nakuru County, which is a human and animal public health concern, hence a need to urgently regulate and monitor the use of antimicrobials in animals.

Superbugs and Bacterial Epidemiology from Wound Infection at Health Institutions in Northeast Ethiopia.

Wound infection plays an important role in the development of chronicity by delaying wound healing, prolonging hospital stay, increasing treatment cost and is responsible for significant morbidity. The aim of this study was to investigate the bacterial epidemiology, multi-drug resistance, and associated risk factors for wound infection at health institutions in Northeast Ethiopia. A facility-based cross-sectional study was conducted from February to April 2021. Demographic, clinical, and risk factor variables were collected using a structured questionnaire. Swabs/pus from wound were collected using sterile applicator swab. Specimens were inoculated on culture media and bacterial isolates were identified using microbiological techniques. Antimicrobial susceptibility test was performed using Kirby-Bauer disc diffusion method. Statistical analysis was done using SPSS software. A total of 229 participants were included in this study. A total of 170 bacterial isolates (74.2%) were isolated. The predominant isolates were S. aureus 80 (47.05%), followed by P. aeruginosa 29 (17.05%), E. coli 22 (12.94%), and Klebsiella spp. 16 (9.41%). Tetracycline (71.7%), clindamycin (15.2%), erythromycin (30.4%), penicillin (80.4%), and co-trimoxazole (80.4%) resistance rates were observed among Gram positive bacterial isolates. The overall prevalence of multi-drug resistance was 71%. Hence, improving the laboratory setup for culture and drug susceptibility testing is recommended for effective treatment of wound infection and to improve infection prevention and control practices in healthcare settings.

Capsular typing of Streptococcus pneumoniae isolated from clinical specimens in Gauhati Medical College and hospital, Assam, India

PurposeStreptococcus pneumoniae is an important human respiratory tract pathogen causing pneumococcal diseases in majority of children and adults. The capsule is a significant virulence factor of Pneumococci which determines the bacterial serotype and is the component used for synthesis of pneumococcal vaccines. This cross-sectional study aimed to isolate Streptococcus pneumoniae from clinical samples and determine the occurrence of its circulating serotypes in Assam, North East India. Materials and methodsA total of 80 clinical samples were collected from June 2019 to May 2020 from patients clinically suspected from pneumococcal infection and also included samples routinely sent to bacteriology laboratory. Isolation and identification of S. pneumoniae was performed using conventional culture and molecular methods. Antibiotic susceptibility patterns were monitored. Capsular serotyping was performed using PCR of cpsA gene followed by DNA sequencing. ResultsMajority of the cases suspected of pneumococcal infection belong to the paediatric group aged less than 5 years. Out of 80 samples, 10 (12.50%) were found to be positive by PCR of recP gene. Culture was positive in 80% (8/10) of the total positives. Co-trimoxazole resistance was seen in 33.33% of the isolate from sputum. Serotypes 6A, 6B, 6C and 19F were detected in our region, out of which 6C is a non-vaccine serotype. ConclusionContinued surveillance is needed to monitor trends in non-vaccine serotypes that may emerge as highly associated with antibiotic resistance. Also, the need to continuous monitoring of the antibiotic susceptibility of S. pneumoniae in North eastern parts of India is of outmost importance.

Nasopharyngeal Carriage Rate of Streptococcus pneumoniae, Related Risk Factors, and Antibiotic Susceptibility Among Inmates in Hawassa Central Prison Institute: Hawassa, Sidama National Region, Ethiopia.

The bacterium Streptococcus pneumoniae commonly causes severe bacterial illnesses in both children and adults. S. pneumoniae is the most fatal bacterial pathogen, causing 50% of the deaths from lower respiratory infections in people of all ages. This study was aimed to determine a nasopharyngeal carriage rate of S. pneumoniae, related risk factors, and antibiotic susceptibility among prisoners in Hawassa Central Prison Institute Hawassa, Ethiopia. From July to August 2021, a cross-sectional investigation was carried out in Hawassa prison. All randomly chosen adult volunteers were a part of the study. In this study, about 330 different people were included. Within 3 h of collection, the swab specimen was inoculated onto 5% sheep blood agar; the inoculated medium was then incubated for 18-24 h at 35-37 °C in a CO2-enriched environment. Following incubation, the S. pneumoniae colonies were suspected, but the usual colony shape, alpha-hemolysis, Gram staining, optochin susceptibility, and bile solubility test allowed for confirmation. Antimicrobial susceptibility testing was carried out in accordance with the Clinical and Laboratory Standards Institute's guidelines. Overall carriage rate of S. pneumoniae among adult individuals were 41 (12.7%). The carriage rate of S. pneumoniae was affected by age classes that 39-48 years (OR = 4.82, 95%CI = 1.49-15.56, p = .009), 49-58 years (OR = 5.27, 95%CI = 1.27-21.89, p = .022), and greater than 58 years (OR = 4.36, 95%CI = 1.13-16.90, p = .033); cigarette smoking (OR = 3.41, 95%CI = 1.16-10.01, p = .026); and sharing beds (OR = 3.91, 95%CI = 1.27-12.07, p = .018). The majority of the isolates are susceptible for clindamycin (87.8%) and resistant for chloramphenicol (56%). Multidrug resistance was observed in 36.7%. The overall carriage rate of S. pneumoniae was 12.7%. Age, cigarette smoking, and sharing beds in the same prison room had a substantial impact on this nasopharyngeal carriage rate. Chloramphenicol (56%), erythromycin (41.5%), tetracycline (39%), and co-trimoxazole (34.1%) resistance were seen in the majority of S. pneumoniae isolates. Early detection, hygiene maintenance, and appropriate treatment are necessary.

Effect and Mechanism of Cotrimoxazole Against Talaromyces marneffei in vitro.

Talaromyces marneffei (formerly Penicillium marneffei) is an important thermally dimorphic fungus endemic which is characterized by one of the most frequent opportunistic infections in HIV/AIDS patients, mainly prevalent in Southeast Asia, southern China, and northeastern India. Cotrimoxazole(CTX) inhibits folic acid synthesis which is important for the survival of many bacteria, protozoa, and fungi, thereby commonly used to prevent several opportunistic infections among HIV/AIDS patients. In addition to preventing other HIV-associated opportunistic infections, CTX prophylaxis are considered to have the potential to prevent T. marneffei infection in HIV/AIDS patients receiving antiretroviral therapy (ART). However, the effect of cotrimoxazole towards T. marneffei fungus in vitro remains unclear. Human THP-1 macrophages were used as cell model in vitro to explore the effect and mechanism of cotrimoxazole resistance towards T. marneffei. Cell viability assay and drug sensitivity colony forming units (CFU) experiments were conducted to determine the minimum inhibitory concentration (MIC) of cotrimoxazole inside and outside THP-1 macrophages respectively. Enzyme-linked immunosorbent assay (Elisa) was used to measure the concentration of Dihydropteroic acid synthetase (DHPS), Dihydrofolate synthetase (DHFS) and Dihydrofolate reductase (DHFR) between T. marneffei adding TMP/SMX and without adding TMP/SMX group respectively. Real-time fluorescence quantitative PCR(qPCR) was performed to detect the mRNA expression levels in Dectin-1 mediated signaling pathway and downstream inflammatory cytokines including IL-6, IL-10, IL-23A, CXCL8 and TNF-α released by T. marneffei-infected macrophages between adding TMP/SMX and without adding TMP/SMX group respectively. Cotrimoxazole can inhibit the proliferation of T. marneffei within safe concentration inside and outside THP-1 macrophages. Drug susceptibility results showed the minimal inhibit concentration(MIC) of 1:5 TMP/SMX was ranging from 14/70 to 68/340μg/ml. The MIC of SMX was ranging from 100 to 360μg/ml. The MIC of TMP was ranging from 240 to 400μg/ml outside macrophages. The MIC of TMP/SMX was ranging from 36/180 to 68/340μg/ml. The MIC of SMX was ranging from 340 to 360μg/ml. The MIC of TMP was ranging from 320 to 400μg/ml inside macrophages. The synergistic interaction of 1:5 TMP/SMX was more effective in inhibiting T. marneffei than separate SMX and TMP. DHPS, DHFS and DHFR can be inhibited by cotrimoxazole within safe and effective concentration. Dectin-1 expression is increased following T. marneffei infection, leading to the increase of IL-6, IL-10, IL-23A and the decrease of CXCL8 and TNF-α. Conversely, cotrimoxazole decrease the levels of Dectin-1, IL-6, IL-10, IL-23A and increase the levels of CXCL8 and TNF-α, thereby enhancing the intracellular killing-T. marneffei capacity of macrophages. Our findings indicated that cotrimoxazole directly inhibited T. marneffei growth by blocking DHPS, DHFS and DHFR and indirectly inhibited T. marneffei growth perhaps by regulating the Dectin-1 signaling pathway, which may effectively interfere with the defense ability of the host against T. marneffei infection.

Cotrimoxazole Resistance Profile of Bacterial Strains Isolated from Urine Samples in Children Born to HIV Positive Mothers Compared to HIV Non-exposed Children

Cotrimoxazole Resistance Profile of Bacterial Strains Isolated from Urine Samples in Children Born to HIV Positive Mothers Compared to HIV Non-exposed Children

Clinical associations with carriage of pulmonary Stenotrophomonas maltophilia.

Stenotrophomonas maltophilia causes opportunistic respiratory infections and is associated with declining lung function in patients with cystic fibrosis (CF). Risk factors for carrying S. maltophilia remain unclear. We conducted a retrospective study of patients yielding ⩾1 respiratory S. maltophilia isolate at the Oxford University Hospitals Trust between 2014 and 2019 and a cohort study of S. maltophilia carriage in CF patients attending annual review in 2018. Seven hundred and forty isolates were identified from 238 patients (median 1.0 isolate/patient). Predisposing conditions included invasive ventilation (29.8%), CF (25.6%) and non-CF bronchiectasis (24.4%). The rates of Stenotrophomonas isolates and co-trimoxazole resistance were stable over time. About 10.8% of isolates were co-trimoxazole-resistant, with resistance more common in CF than in other diagnoses (29.5% vs 5.8%, p < 0.001). No clinical features were significantly associated with S. maltophilia carriage in the CF population. We present new insight into the epidemiology of Stenotrophomonas colonisation/infection and identify increased co-trimoxazole resistance in CF isolates.

Molecular Characterization of MCR-1 Producing Enterobacterales Isolated in Poultry Farms in the United Arab Emirates.

Data on the prevalence of MCR-producing Enterobacterales of animal origin are scarce from the Arabian Peninsula. We investigated the presence and variety of such strains from fecal specimens of poultry collected in four farms in the United Arab Emirates. Colonies from ten composite samples per farm grown on colistin-supplemented plates were PCR-screened for alleles of the mcr gene. Thirty-nine isolates selected based on species, colony morphology, and plasmid profile were subjected to whole genome sequencing. The panel of their resistance and virulence genes, MLST and cgMLST were established. Transferability and incompatibility types of the MCR-plasmids were determined. mcr-1.1 positive strains were identified in 36 of the 40 samples. Thirty-four multi-drug resistant Escherichia coli of 16 different sequence types, two Escherichia albertii, two Klebsiella pneumoniae and one Salmonella minnesota were identified. Beyond various aminoglycoside, tetracycline, and co-trimoxazole resistance genes, seven of them also carried ESBL genes and one blaCMY-2. Six IncHI2, 26 IncI2 and 4 IncX4 MCR-plasmids were mobilized, in case of the IncHI2 plasmids co-transferring ampicillin, chloramphenicol and tetracycline resistance. The diversity of mcr-1 positive strains suggest a complex local epidemiology calling for a coordinated surveillance including animals, retail meat and clinical cases.

Molecular Epidemiology of Multidrug-Resistant Pneumococci among Ghanaian Children under Five Years Post PCV13 Using MLST.

Antibiotic resistance in pneumococci contributes to the high pneumococcal deaths in children. We assessed the molecular characteristics of multidrug-resistant (MDR) pneumococci isolated from healthy vaccinated children under five years of age in Cape Coast, Ghana. A total of 43 MDR isolates were selected from 151 pneumococcal strains obtained from nasopharyngeal carriage. All isolates were previously serotyped by multiplex PCR and Quellung reaction. Susceptibility testing was performed using either the E-test or disk diffusion method. Virulence and antibiotic resistance genes were identified by PCR. Molecular epidemiology was analyzed using multilocus sequence typing (MLST). Vaccine-serotypes 23F and 19F were predominant. The lytA and pavB virulence genes were present in all isolates, whiles 14–86% of the isolates carried pilus-islets 1 and 2, pcpA, and psrP genes. Penicillin, tetracycline, and cotrimoxazole resistance were evident in >90% of the isolates. The ermB, mefA, and tetM genes were detected in (n = 7, 16.3%), (n = 4, 9.3%) and (n = 43, 100%) of the isolates, respectively. However, >60% showed alteration in the pbp2b gene. MLST revealed five novel and six known sequence types (STs). ST156 (Spain9V-3) and ST802 were identified as international antibiotic-resistant clones. The emergence of international-MDR clones in Ghana requires continuous monitoring of the pneumococcus through a robust surveillance system.

Biofilm Formation in Methicillin-Resistant and Methicillin-Sensitive Staphylococcus aureus Strains

Background: The combination of methicillin resistance (MR) and the ability of biofilm formation of Staphylococcus aureus (SA) makes treatment difficult. Biofilm is formed by distinct genetic mechanisms in MRSA and methicillin-sensitive SA (MSSA), and hence, there is difference in the prevalence of biofilms in them. This study investigated the biofilm production in SA and analyzed its correlation with MR. Materials and methods: A total of 261 consecutive Staphylococcus aureus isolated from various clinical samples from January to April 2019 were included in the study. Antibiotic sensitivity was carried out as per Clinical and Laboratory Standards Institute guidelines and cefoxitin disk was used for screening for MR. Total of 147 MSSA and 114 MRSA were taken for further processing. Biofilm formation was determined by tube and microtiter plate methods in all the isolates. The data were analyzed for statistical significance using Microsoft excel software. Results: Resistance to erythromycin, clindamycin, gentamicin, cotrimoxazole, and inducible clindamycin resistance was significantly higher in all the MR Staphylococcus strain including biofilm forming MRSA strains. The biofilm formation was significantly higher in MSSA isolates by both the tube (78.2%) and microtiter plate methods (64.9%). Discussion: Although the antimicrobial resistance was higher in MRSA, the ability to form biofilms was significantly higher in MSSA. Biofilms of MSSA are usually less prevalent than MRSA probably because of the distinct genetic mechanisms involved in the formation of biofilms. The higher biofilm forming ability of MSSA in our study highlights the need for determination of other genes involved in biofilm formation and virulence mechanisms in SA.

Comparison of Consumption Data and Phenotypical Antimicrobial Resistance in E. coli Isolates of Human Urinary Samples and of Weaning and Fattening Pigs from Surveillance and Monitoring Systems in Germany.

Antimicrobial resistance (AMR) data from humans are mostly collected from clinical isolates, whereas from livestock data also exist from colonizing pathogens. In Germany, livestock data are collected from clinical and nonclinical isolates. We compared resistance levels of clinical and nonclinical isolates of Escherichia coli from weaning and fattening pigs with clinical outpatient isolates of humans from urban and rural areas. We also studied the association of AMR with available antimicrobial use (AMU) data from humans and pigs. Differences between rural and urban isolates were minor and did not affect the comparison between human and pig isolates. We found higher resistance levels to most antimicrobials in human isolates compared to nonclinical isolates of fattening pigs. Resistance to ampicillin, however, was significantly more frequent in clinical isolates of fattening pigs and in clinical and nonclinical isolates of weaning pigs compared to isolates from humans. The opposite was observed for ciprofloxacin. Co-trimoxazole resistance proportions were higher in clinical isolates of weaning and fattening pigs as compared to isolates from humans. Resistance proportions were higher in clinical isolates than in nonclinical isolates from pigs of the same age group and were also higher in weaner than in fattening pigs. Significant associations of AMU and AMR were found for gentamicin resistance and aminoglycoside use in humans (borderline) and for ampicillin resistance in clinical isolates and penicillin use in fattening pigs. In summary, we found significant differences between isolates from all populations, requiring more detailed analyses supported by molecular data and better harmonized data on AMU and AMR.

Genomic surveillance of invasive Streptococcus pneumoniae isolates in the period pre-PCV10 and post-PCV10 introduction in Brazil.

In 2010, Brazil introduced the 10-valent pneumococcal conjugate vaccine (PCV10) into the national children’s immunization programme. This study describes the genetic characteristics of invasive Streptococcus pneumoniae isolates before and after PCV10 introduction. A subset of 466 [pre-PCV10 (2008–2009): n=232, post-PCV10 (2012–2013): n=234;<5 years old: n=310, ≥5 years old: n=156] pneumococcal isolates, collected through national laboratory surveillance, were whole-genome sequenced (WGS) to determine serotype, pilus locus, antimicrobial resistance and genetic lineages. Following PCV10 introduction, in the <5 years age group, non-vaccine serotypes (NVT) serotype 3 and serotype 19A were the most frequent, and serotypes 12F, 8 and 9 N in the ≥5 years old group. The study identified 65 Global Pneumococcal Sequence Clusters (GPSCs): 49 (88 %) were GPSCs previously described and 16 (12 %) were Brazilian clusters. In total, 36 GPSCs (55 %) were NVT lineages, 18 (28 %) vaccine serotypes (VT) and 11 (17 %) were both VT and NVT lineages. In both sampling periods, the most frequent lineage was GPSC6 (CC156, serotypes 14/9V). In the <5 years old group, a decrease in penicillin (P=0.0123) and cotrimoxazole (P<0.0001) resistance and an increase in tetracycline (P=0.019) were observed. Penicillin nonsusceptibility was predicted in 40 % of the isolates; 127 PBP combinations were identified (51 predicted MIC≥0.125 mg l−1); cotrimoxazole (folA and/or folP alterations), macrolide (mef and/or ermB) and tetracycline (tetM, tetO or tetS/M) resistance were predicted in 63, 13 and 21.6 % of pneumococci studied, respectively. The main lineages associated with multidrug resistance in the post-PCV10 period were composed of NVT, GPSC1 (CC320, serotype 19A), and GPSC47 (ST386, serotype 6C). The study provides a baseline for future comparisons and identified important NVT lineages in the post-PCV10 period in Brazil.

Bacterial Etiologies of Ear Infection and Their Antimicrobial Susceptibility Pattern at the University of Gondar Comprehensive Specialized Hospital, Gondar, Northwest Ethiopia: A Six-Year Retrospective Study.

BackgroundAn ear infection is responsible for up to 40% of preventable hearing impairment; one of the reasons for frequent and unwise antibiotic usage, especially in the developing world. Since the incidence of antibiotic resistance is increasing, especially in resource-limited countries, up-to-date knowledge on the susceptibility of ear-discharge isolates to antibiotic is important for better patient treatment. Therefore, this study aimed at determining the bacterial etiologies and their antibiotic susceptibility profiles among patients suspected with ear infections.MethodsWe collected retrospective data from bacteriological results of ear discharge samples from 2013 to 2018. Sample collection, culture preparation, and bacterial identification were performed using standard microbiological techniques. Antimicrobial susceptibility testing was performed following Clinical and Laboratory Standard Institute (CLSI) guidelines. We extracted and inputted the data using Epi-info version 7 and exported it to SPSS version 20 for analysis.ResultsThe overall ear-discharge culture positivity rate was 283/369 (76.7%) (95% CI = 72.4–81.3), with 14/283 (4.95%) mixed infections. Staphylococcus aureus (27.9%), Proteus spps (20.8%), Streptococcus spps (10%), and Pseudomonas spps (8.92%) were the main isolates. High-level resistance rates for tetracycline (77.6%), penicillins (67.2%), erythromycin (52.6%), and co-trimoxazole (52%), and low-level resistance rates for fluoroquinolones (23.3%), aminoglycosides (23.7%), and cephalosporins (29.8%) were observed. More than 45% of isolates, with 50.9% of Gram-negative and 37.3% of Gram-positive, were multidrug-resistant.ConclusionStaphylococcus aureus, Proteus mirabilis, Proteus vulgaris, Escherichia coli, and Pseudomonas aeruginosa were the leading cause of ear infections. The presence of high number of multidrug-resistant strains calls for the need for periodic and continuous follow-up of antibiotic usage in the study area. Further studies are recommended to explore the types of ear infections, with their etiologic agents and possible risk factors.

Genomic Diversity and Antimicrobial Resistance of Haemophilus Colonizing the Airways of Young Children with Cystic Fibrosis.

Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae and Haemophilus parainfluenzae are routinely isolated from the lungs of children with CF; however, little is known about the frequency and characteristics of Haemophilus colonization in this context. Here, we describe the detection, antimicrobial resistance (AMR), and genome sequencing of H. influenzae and H. parainfluenzae isolated from airway samples of 147 participants aged ≤12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program, Melbourne, Australia. The frequency of colonization per visit was 4.6% for H. influenzae and 32.1% for H. parainfluenzae, 80.3% of participants had H. influenzae and/or H. parainfluenzae detected on at least one visit, and using genomic data, we estimate 15.6% of participants had persistent colonization with the same strain for at least two consecutive visits. Isolates were genetically diverse and AMR was common, with 52% of H. influenzae and 82% of H. parainfluenzae displaying resistance to at least one drug. The genetic basis for AMR could be identified in most cases; putative novel determinants include a new plasmid encoding blaTEM-1 (ampicillin resistance), a new inhibitor-resistant blaTEM allele (augmentin resistance), and previously unreported mutations in chromosomally carried genes (pbp3, ampicillin resistance; folA/folP, cotrimoxazole resistance; rpoB, rifampicin resistance). Acquired AMR genes were more common in H. parainfluenzae than H. influenzae (51% versus 21%, P = 0.0107) and were mostly associated with the ICEHin mobile element carrying blaTEM-1, resulting in more ampicillin resistance in H. parainfluenzae (73% versus 30%, P = 0.0004). Genomic data identified six potential instances of Haemophilus transmission between participants, of which three involved participants who shared clinic visit days. IMPORTANCE Cystic fibrosis (CF) lung disease begins during infancy, and acute respiratory infections increase the risk of early disease development and progression. Microbes involved in advanced stages of CF are well characterized, but less is known about early respiratory colonizers. We report the population dynamics and genomic determinants of AMR in two early colonizer species, namely, Haemophilus influenzae and Haemophilus parainfluenzae, collected from a pediatric CF cohort. This investigation also reveals that H. parainfluenzae has a high frequency of AMR carried on mobile elements that may act as a potential reservoir for the emergence and spread of AMR to H. influenzae, which has greater clinical significance as a respiratory pathogen in children. This study provides insight into the evolution of AMR and the colonization of H. influenzae and H. parainfluenzae in a pediatric CF cohort, which will help inform future treatment.

Salmonella Typhi from Northwest Pakistan: Molecular Strain Typing and Drug Resistance Signature.

Objective: To determine the molecular strain typing and drug resistance pattern of Salmonella enterica serovar Typhi prevalent in Northwest Pakistan. Methodology: A total of 2,138 blood samples of suspected typhoid patients from Northwest Pakistan were collected followed by identification of Salmonella Typhi through biochemical, serological, and species-specific fliC-d gene amplification. These isolates were typed by variable-number tandem repeat (VNTR) profiling and investigated for drug resistance. Results: The overall prevalence of Salmonella Typhi was found to be 8.8% (n = 189). Thirty different VNTR strain types of Salmonella Typhi were detected and the most prevalent strain types were T1 and T4, whereas T27 was less prevalent strain. Among the 189 isolates 175 (92.5%) isolates were multidrug resistant, whereas 12 (5.8%) isolates were extensively drug resistant. Resistance to imipenem in Salmonella Typhi was not observed. Most of the isolates have genes encoding for resistance to fluoroquinolones, including gyrA (n = 164), gyrB (n = 160), parC (n = 164), parE (n = 160), ac(6')-ib-cr (n = 163), qnrS (n = 15), and qnrB (n = 3). Similarly, chloramphinicol (cat; n = 147), azithromycin (msrA; n = 3), and co-trimoxazole (dfrA7; n = 145) resistance genes were detected among Salmonella Typhi isolates. Conclusion: In this study, T1 and T4 type Salmonella Typhi strains were predominantly prevalent in Northwest Pakistan. Antibiotic resistance among Salmonella Typhi isolates were observed. Findings of the study would be helpful to devise an appropriate antibiotic policy to control the emergence of drug-resistant Salmonella Typhi in Pakistan.

Genome-wide analysis of urogenital and respiratory multidrug-resistant Haemophilus parainfluenzae.

To characterize the mechanisms of antimicrobial resistance and the prevalence of the polysaccharide capsule among urogenital and respiratory Haemophilus parainfluenzae isolates. Antimicrobial susceptibility was tested by microdilution. Fifty-five MDR strains were subjected to WGS and were phylogenetically compared with all the available H. parainfluenzae genomes from the NCBI database. The identification of the capsular bexA gene was performed by PCR in 266 non-MDR strains. In 31 of the 42 ampicillin-resistant strains, blaTEM-1 located within Tn3 was identified. β-Lactamase-negative cefuroxime-resistant strains (n = 12) presented PBP3 substitutions. The catS gene (n = 14), the tet(M)-MEGA element (n = 18) and FolA substitutions (I95L and F154V/S) (n = 41) were associated with resistance to chloramphenicol, tetracycline plus macrolides, and co-trimoxazole, respectively. Thirty-seven isolates had a Tn10 harbouring tet(B)/(C)/(D)/(R) genes with (n = 15) or without (n = 22) catA2. Putative transposons (Tn7076-Tn7079), including aminoglycoside and co-trimoxazole resistance genes, were identified in 10 strains (18.2%). These transposons were integrated into three new integrative and conjugative elements (ICEs), which also included the resistance-associated transposons Tn3 and Tn10. The capsular operon was found only in the urogenital isolates (18/154, 11.7%), but no phylogenetic clustering was observed. The capsular operons identified were similar to those of Haemophilus influenzae serotype c and Haemophilus sputorum type 2. The identification of ICEs with up to three resistance-associated transposons suggests that these transferable elements play an important role in the acquisition of multidrug resistance in H. parainfluenzae. Moreover, the presence of polysaccharide capsules in some of these urogenital isolates is a cause for concern.