Genotypic Resistance Patterns Research Articles

Phenotypic and genotypic antimicrobial resistance patterns in honey bee (Apis mellifera L.) bacterial symbionts.

Antimicrobial resistance (AMR) is a major global public health problem. Nevertheless, the knowledge of the factors driving the spread of resistance among environmental microorganisms is limited, and few studies have been performed worldwide. Honey bees (Apis mellifera L.) have long been considered bioindicators of environmental pollution and more recently also of AMR. In this study, 53 bacterial strains isolated from the body surface of honey bees at three ontogenetic stages, collected from ten different geographic locations, were tested for their phenotypic and genotypic resistance to eight classes of the most widely used antimicrobials in human and veterinary medicine. Results showed that 83% of the strains were resistant to at least one antimicrobial and 62% were multidrug-resistant bacteria, with a prevalence of resistance to nalidixic acid, cefotaxime, and aztreonam. A high percentage of isolates harbouring at least one antimicrobial gene was also observed (85%). The gene encoding resistance to colistin mcr-1 was the most abundant, followed by those for tetracycline tetM and tetC. Geographical features influenced the distribution of these traits more than bacterial species or bee stage, supporting the use of honey bee colonies and their associated bacteria as indicators to monitor environmental resistance. This approach can improve the scientific understanding of this global threat by increasing data collection capacity.

Phenotypic and Genotypic Antibiotic Resistance Patterns of Clinical Shigella Isolates from Tehran, Iran

Background: The emergence of multidrug-resistant (MDR) Shigella is a health concern in both developed and developing countries. The indiscriminate use of antibiotics without considering resistance patterns has led to the emergence of resistant strains. Objectives: This study aimed to investigate the phenotypic and genotypic patterns of antibiotic resistance and virulence gene distribution in Shigella isolates from patients in Tehran, Iran. Methods: In this cross-sectional study, 60 Shigella isolates were collected from patients referred to Milad Hospital and Pasargad Laboratory in Tehran. The isolates were gathered over four months, from February 2023 to June 2023. After biochemical and genetic confirmation of the isolates, the disk diffusion method was employed to determine antibiotic resistance patterns. The distribution of beta-lactamase genes (blaCTX-M1, blaCTX-M2, blaCTX-M8, blaSHV, blaTEM, and blaOXA) and virulence genes (ial, virF, invE, sigA, and pic) was investigated in Shigella isolates using the multiplex PCR method. SPSS statistical software version 22 was used for data analysis. Results: Thirty-six percent of isolates were found to be MDR. The highest rate of resistance was against tetracycline (90%) and ampicillin (80%). The lowest resistance rate was against azithromycin (1.9%) and amikacin (7.1%). The blaCTX-M1 and blaCTX-M8 genes were more prevalent, detected in 38.3% and 50% of the isolates, respectively. However, the blaSHV and blaCTX-M2 genes were not detected in any of the isolates. Additionally, 32% of the MDR isolates harbored both the blaCTX-M1 and blaCTX-M8 genes simultaneously. The distribution of virulence genes ial, virF, invE, sigA, and pic in the studied isolates was 28.3%, 85%, 68.3%, 81.7%, and 15%, respectively. Conclusions: The present study emphasizes the increasing trend of MDR Shigella isolates. Therefore, serious measures are needed to prevent the spread of resistant genes. Furthermore, the detection of virulence factors could help in controlling shigellosis, which is a significant global health issue.

Emergence of multidrug-resistant Bacillus spp. derived from animal feed, food and human diarrhea in South-Eastern Bangladesh

BackgroundAntimicrobial resistance poses a huge risk to human health worldwide, while Bangladesh is confronting the most severe challenge between the food supply and the huge consumption of antibiotics annually. More importantly, probiotics containing Bacillus spp. are claimed to be an alternative to antimicrobial stewardship programs. However, their antibiotic resistance remains elusive. Thus, we employed the antimicrobial susceptibility test and PCR to assess the prevalence of resistance, including multidrug resistance (MDR) and resito-genotyping of isolated Bacillus spp.ResultsThe phenotypic profile showed that Bacillus spp. were 100% sensitive to gentamicin (2 µg/mL), whereas lowered sensitivity to levofloxacin (67.8%, 0.5–1 µg/mL), ciprofloxacin (62.3%, 0.5–1 µg/mL), clindamycin (52.2%, 0.25–0.5 µg/mL), amoxicillin-clavulanic acid (37.6%, 0.06 µg/mL), azithromycin (33.4%, 1–2 µg/mL), tetracycline (25.6%, 2–4 µg/mL), nitrofurantoin (21.1%, 16–32 µg/mL), co-trimoxazole (19.2%, 2 µg/mL), and erythromycin (18.8%, 0.25–0.5 µg/mL). The strains were completely resistant to penicillin, amoxicillin-clavulanic acid, cefixime, ceftriaxone, vancomycin, and co-trimoxazole, and a species-specific trend was seen in both phenotypic and genotypic resistance patterns. Genotypic resistance indicated prevalence of the bla1 (71.5%), tetA (33%), erm1 (27%), blaTEM (13.1%), blaCTX-M-1/blaCTX-M-2 /sul1 (10.1%), blaSHV (9.6%), and qnrS (4.1%) genes. The β-lactamase resistance gene bla1 was found in all penicillin-resistant (MIC ≥ 32 µg/mL) Bacillus spp. One hundred ninety-one isolates (89.6%) were MDR, with 100% from diarrhea, 90.3% from food, and 88.7% from animal feed.ConclusionBased on the MIC value and profile analysis of antibiotic resistance genes, this is the first study that Bacillus spp. antimicrobial susceptibilities have been identified in Bangladesh, and our study will shed light on the adverse effects of feed-borne Bacillus spp. emerging from animal feed to the food chain. A comprehensive investigation is urgently needed by policymakers on tolerance limits and harmful effects in the animal industry.

Genotypic and phenotypic drug resistance patterns of Mycobacterium tuberculosis isolated from presumptive pulmonary tuberculosis patients in Ethiopia: A multicenter study.

The emergence of drug-resistant tuberculosis (DR-TB) has been a major obstacle to global tuberculosis control programs, especially in developing countries, including Ethiopia. This study investigated drug resistance patterns and associated mutations of Mycobacterium tuberculosis Complex (MTBC) isolates from the Amhara, Gambella, and Benishangul-Gumuz regions of Ethiopia. A cross-sectional study was conducted using 128 MTBC isolates obtained from patients with presumptive tuberculosis (TB). Phenotypic (BACTEC MGIT 960) and genotypic (MTBDRplus and MTBDRsl assays) methods were used for drug susceptibility testing. Data were entered into Epi-info and analyzed using SPSS version 25. Frequencies and proportions were determined to describe drug resistance levels and associated mutations. Of the 127 isolates recovered, 100 (78.7%) were susceptible to four first-line anti-TB drugs. Any drug resistance, polydrug resistance, and multi-drug resistance (MDR) were detected in 21.3% (27), 15.7% (20), and 15% (19) of the isolates, respectively, by phenotypic and/or genotypic methods. Mono-resistance was observed for Isoniazid (INH) (2, 1.6%) and Streptomycin (STR) (2, 1.6%). There were two genotypically discordant RIF-resistant cases and one INH-resistant case. One case of pre-extensively drug-resistant TB (pre-XDR-TB) and one case of extensively drug-resistant TB (XDR-TB) were identified. The most frequent gene mutations associated with INH and rifampicin (RIF) resistance were observed in the katG MUT1 (S315T1) (20, 76.9%) and rpoB (S531L) (10, 52.6%) genes, respectively. Two MDR-TB isolates were resistant to second-line drugs; one had a mutation in the gyrA MUT1 gene, and the other had missing gyrA WT1, gyrA WT3, and rrs WT1 genes without any mutation. The detection of a significant proportion of DR-TB cases in this study suggests that DR-TB is a major public health problem in Ethiopia. Thus, we recommend the early detection and treatment of DR-TB and universal full first-line drug-susceptibility testing in routine system.

The phenotypic and genotypic antimicrobial resistance patterns of Salmonella isolated from chickens and meat at poultry slaughterhouses in Japan and Thailand.

Poultry meat is a popular food consumed globally. However, poultry farming is a source of Salmonella contamination which causes human salmonellosis. This study aimed to estimate the prevalence and antimicrobial resistance (AMR) of Salmonella among chickens and meat at poultry slaughterhouses in province study areas in Thailand and Japan. Chicken meat and feces samples were collected in Thailand and Japan. In Nakhon Ratchasima Province, Thailand, 558 samples were obtained from slaughterhouses from January 2021 to March 2022. In Gifu Prefecture, Japan, 140 samples (70 each of intestinal contents and meat) were purchased from slaughterhouses from June to October 2022. For Salmonella detection, the samples were cultivated according to the International Organization for Standardization 6579:2002/AMD 1:2007 method and confirmed using polymerase chain reaction (PCR) and agglutination tests for serotyping. Isolated Salmonella were tested for AMR to nine antibiotics using the disk diffusion method. Selected phenotypic multidrug-resistant (MDR) isolates were evaluated for AMR genes (AMRGs) using PCR. Salmonella prevalence from chickens and meat at slaughterhouses in Thailand and Japan was 41.2% and 40.7%, respectively. All the Salmonella isolates in Japan were serotyped as Schwarzengrund, and no Salmonella isolates were resistant to the nine antibiotics tested. In contrast, most of the Thai Salmonella isolates from chicken cloacal swabs and meat were resistant to doxycycline (78.3%) and colistin (63.5%). The prevalence of MDR Salmonella (MDRS) in chickens and meat from Thailand and Japan was 29.1% (67/230) and 0% (0/57), respectively. However, the most frequent AMRGs found in MDRS in Thailand were extended-spectrum beta-lactamase-Temoneira (ESBL-TEM) (45.1%). All isolated Salmonella from Japan revealed a class 1 integron gene (Int-1). Phenotypic MDRS isolates from Thailand showed the greatest correlation to AMRG and ESBL-TEM. Although there were no phenotypic AMR Salmonella isolates found in Japan, they can be found associated with Int-1, which may carry other AMRGs within the gene cassettes.

Molecular detection of Helicobacter pylori and its genotypic antimicrobial resistance patterns in dyspeptic Mozambican patients

AbstractBackgroundHelicobacter pylori strains show a high level of genotypic diversity and express several genes that contribute to their pathogenicity and resistance. In Mozambique, there is lack of information regarding its resistance pattern to antibiotics. In this study, we aimed to investigate the prevalence of H. pylori and its genotypic resistance to clarithromycin, metronidazole, and fluoroquinolones in Mozambican dyspeptic patients. Since appropriate eradication should be based on the local resistance rate, our data will guide clinicians in choosing the best drugs for the effective treatment of H. pylori‐infected patients.MethodsThis is a cross‐sectional descriptive study conducted between June 2017 and June 2020, in which 171 dyspeptic patients were recruited, and through upper gastrointestinal endoscopy, gastric biopsies were collected from those patients. Polymerase chain reaction was performed for the detection of H. pylori and its resistance mechanisms to clarithromycin (23S rRNA), metronidazole (rdxA), and fluoroquinolones (gyrA); mutations conferring resistance to these antibiotics were investigated by sequencing 23S rRNA, rdxA, and gyrA genes.ResultsOf the 171 samples tested, H. pylori was detected in 56.1% (96/171). The clarithromycin resistance rate was 10.4% (the responsible mutations were A2142G and A2143G), the metronidazole resistance rate was 55.2% (4 types of mutations responsible for metronidazole resistance were identified which include, D59N, R90K, H97T, and A118T. However, in many cases, they appeared in combination, with D59N + R90K + A118T being the most frequent combination), and the fluoroquinolones resistance rate was 20% (the responsible mutations were N87I and D91G).ConclusionH. pylori infection remains common in dyspeptic Mozambican patients. High resistance to metronidazole and fluoroquinolones requires continuous monitoring of antibiotic resistance and adaptation of therapy to eradicate this infection.

Insight into Population Structure and Drug Resistance of Pediatric Tuberculosis Strains from China and Russia Gained through Whole-Genome Sequencing.

This study aimed to determine phenotypic and genotypic drug resistance patterns of Mycobacterium tuberculosis strains from children with tuberculosis (TB) in China and Russia, two high-burden countries for multi/extensively-drug resistant (MDR/XDR) TB. Whole-genome sequencing data of M. tuberculosis isolates from China (n = 137) and Russia (n = 60) were analyzed for phylogenetic markers and drug-resistance mutations, followed by comparison with phenotypic susceptibility data. The Beijing genotype was detected in 126 Chinese and 50 Russian isolates. The Euro-American lineage was detected in 10 Russian and 11 Chinese isolates. In the Russian collection, the Beijing genotype and Beijing B0/W148-cluster were dominated by MDR strains (68% and 94%, respectively). Ninety percent of B0/W148 strains were phenotypically pre-XDR. In the Chinese collection, neither of the Beijing sublineages was associated with MDR/pre-XDR status. MDR was mostly caused by low fitness cost mutations (rpoB S450L, katG S315T, rpsL K43R). Chinese rifampicin-resistant strains demonstrated a higher diversity of resistance mutations than Russian isolates (p = 0.003). The rifampicin and isoniazid resistance compensatory mutations were detected in some MDR strains, but they were not widespread. The molecular mechanisms of M. tuberculosis adaptation to anti-TB treatment are not unique to the pediatric strains, but they reflect the general situation with TB in Russia and China.

Detection of Antimicrobial Resistance Genes from Shiga Toxin Producing Escherichia coli by Multiplex PCR

Background: Shiga toxin-producing Escherichia coli (STEC) strains are considered to be most common food-borne enteric zoonotic pathogen, causing various disease conditions in both animals and humans and are highly pathogenic to human in low infectious doses. Resistance against antibiotics by STEC is also a big concern now a days. Hence in view of the public health significance of STEC, present work was planned to know the combination of phenotypic and genotypic resistance patterns against certain most commonly used antibiotics by using disk diffusion method and multiplex PCR respectively. Methods: A total of 426 PCR confirmed STEC isolates isolated from pooled samples (animal faecal(179), farm water(122) and human faecal samples (125) of different livestock farms in and around Proddatur andhra Pradesh, were subjected to antibiotic sensitivity test by using disc diffusion method. The isolates that showed resistance for tetracycline, streptomycin, sulphonamides and ampicillin were selected and subjected to multiplex PCR for the detection of resistance genes. Result: Disk diffusion assay revealed highest phenotypic resistance for STEC isolates against Cepahlothin (100%), followed by Ampicillin (99.06%), Tetracycline (97.2%), Streptomycin (94.3%), Sulphonamides (90.8%) and Trimethoprim (84.5%). Pooled samples also revealed the presence of antimicrobial resistance genes like tetA(59.2%), tetB(43.5%), tetC (9.2%), strA (39.3%), strB(54.1%), sul1 (40.8%), sul2 (58.7%), sul3 (3.8%) and blaTEM(83.4%). These findings indicate the highest prevalence of antimicrobial resistance among the STEC isolates, which alarms indiscriminate use of antibiotics both for therapeutic purpose and as growth promoters. Strict hygienic, sanitation and HACCP programmes should be applied to counter STEC prevalence.

A pandemic within a pandemic? Admission to COVID-19 wards in hospitals is associated with increased prevalence of antimicrobial resistance in two African settings

BackgroundPatients who develop severe illness due to COVID-19 are more likely to be admitted to hospital and acquire bacterial co-infections, therefore the WHO recommends empiric treatment with antibiotics. Few reports have addressed the impact of COVID-19 management on emergence of nosocomial antimicrobial resistance (AMR) in resource constrained settings. This study aimed to ascertain whether being admitted to a COVID-19 ward (with COVID-19 infection) compared to a non-COVID-19 ward (as a COVID-19 negative patient) was associated with a change in the prevalence of bacterial hospital acquired infection (HAI) species or resistance patterns, and whether there were differences in antimicrobial stewardship (AMS) and infection prevention and control (IPC) guidelines between COVID-19 and non-COVID-19 wards. The study was conducted in Sudan and Zambia, two resource constrained settings with differing country-wide responses to COVID-19.MethodsPatients suspected of having hospital acquired infections were recruited from COVID-19 wards and non-COVID-19 wards. Bacteria were isolated from clinical samples using culture and molecular methods and species identified. Phenotypic and genotypic resistance patterns were determined by antibiotic disc diffusion and whole genome sequencing. Infection prevention and control guidelines were analysed for COVID-19 and non-COVID-19 wards to identify potential differences.Results109 and 66 isolates were collected from Sudan and Zambia respectively. Phenotypic testing revealed significantly more multi-drug resistant isolates on COVID-19 wards in both countries (Sudan p = 0.0087, Zambia p = 0.0154). The total number of patients with hospital acquired infections (both susceptible and resistant) increased significantly on COVID-19 wards in Sudan, but the opposite was observed in Zambia (both p = ≤ 0.0001). Genotypic analysis showed significantly more β-lactam genes per isolate on COVID-19 wards (Sudan p = 0.0192, Zambia p = ≤ 0.0001).ConclusionsChanges in hospital acquired infections and AMR patterns were seen in COVID-19 patients on COVID-19 wards compared to COVID-19 negative patients on non-COVID-19 wards in Sudan and Zambia. These are likely due to a potentially complex combination of causes, including patient factors, but differing emphases on infection prevention and control, and antimicrobial stewardship policies on COVID-19 wards were highlighted.

Phenotypic and Genotypic Characterization of Klebsiella pneumoniae isolated from Clinical Mastitis in Buffaloes

Mastitis is the most common serious and economical disease affecting the dairy industry. The current study aimed to determine the molecular characterization of K. pneumoniae isolated from buffaloes with clinical mastitis as well as determine the antimicrobial pattern and virulence associated genes. Out of examination one hundred and fifty dairy buffaloes at Beheria governorate, 57 (38%) showed clinical mastitis signs. All samples are submitted to bacteriological examination and confirmed by biochemical tests. The result showed that K.pneumoniae was identified in only five (8.7%). Regarding to the antibiogram profile, K. pneumoniae isolates exhibited high resistance pattern against Carbenicillin, Cefotaxime, Flumequine, Gentamicin, Kanamycin (100%) followed by Neomycin, Nitrofurantoin, Penicillin (80%) and Oxytetracycline, Sulfamethoxazole / trimethoprim (60%). Meanwhile, higher susceptibility to Ampicillin (100%), followed by Chloramphenicol, Colistin Sulphate, Erythromycin, and Streptomycin (80%). Molecular identification using the mPCR approach applied efficiently to detect the K. pneumoniae virulence genes (mrkA, mrkD, iutA) at 475, 226, 300bp respectively. In addition, the successfully detection of blaTEM and blaSHV for β lactams resistance genes at 516 and 392 bp. In conclusion, the phenotypic and genotypic resistance pattern of K. pneumoniae isolates indicates the portability of transmission of resistance genes through milk and food chain with public health concern.

137. Comparison of genotypic resistance pattern between Enterococcus faecium and Enterococcus faecalis to better understand the occurrence of mutations.

Abstract Background Enterococcus is one of the major causes of nosocomial infections many with vancomycin resistance. About 50,000 infections are reported per year due to vancomycin-resistant Enterococci. Understanding the genotypic mutations can help recognize the potential burden for antibiotic resistance that exists in a population. In this study, using whole genome sequencing (WGS) we aim to analyze the prevalence of genetic resistance markers for commonly used antibiotics for Enterococcal treatment. Methods Whole genome sequencing was performed using the NextSeq (Illumina Inc., CA) on 60 isolates of E. faecium and 29 isolates of E. faecalis. The isolates were obtained from two different Detroit area hospitals from 2017-2019. The data from WGS was analyzed using EPISEQ CSTM (BIOMÉRIEUX, Marcy l ‘Etoile, France) bioinformatic database to obtain specific resistance genes which would correspond to commonly used antibiotics for treatment of Enterococcal infections. Results Among the 89 Enterococcus faecium and Enterococcus faecalis investigated, we identified a total of 33 unique resistance genes across 18 classes of antibiotics (Table 1). We detected genetic mutations efmA, pbp5, tet(L), liar, liaS unique to E. faecium and only emeA unique to E. faecalis. E. faecium and E. faecalis share 14 similar resistance genes. E. faecium and E. faecalis had 12 and 7 unique resistance genes, respectively but are of same drug classes. The most common antibiotic classes include aminoglycosides, tetracyclines, quinolones, beta-lactams, glycopeptides, macrolides, and pyrimidine analogs. Table 1:Enterococcus faecium and E. faecalis genetic mutations and drug class resistance Conclusion Enterococcus faecium had a greater number of resistance genes with glycopeptide, aminoglycoside, and beta lactam resistance when compared to Enterococcus faecalis. Whereas Enterococcus faecalis had more resistance genes associated with macrolides, tetracyclines, pyrimidine analogs, and Bactrim. In general, both appear to have many genes that encode for resistance to major classes of antibiotics which are used for treatment of Enterococcal infections. Further comparison with phenotypic susceptibility testing data would help better understand the practical implications of our resistance gene testing. Disclosures Piyali Chatterjee, PhD, AHRQ Grant # 1R03HS027667-01: Grant/Research Support|AHRQ Grant # 1R03HS027667-01: Central Texas Veterans Health Care System Keith S. Kaye, MD, MPH, Allecra: Advisor/Consultant|GlaxoSmithKline plc.: Receiving symposia honoraria|GlaxoSmithKline plc.: GlaxoSmithKline plc.-sponsored study 212502|Merck: Advisor/Consultant|qpex: Advisor/Consultant|Shionogi: Grant/Research Support|Spero: Advisor/Consultant Chetan Jinadatha, MD, MPH, AHRQ R01 Grant-5R01HS025598: Grant/Research Support|EOS Surfaces: Copper Coupons and materials for testing.

A First Report of Molecular Typing, Virulence Traits, and Phenotypic and Genotypic Resistance Patterns of Newly Emerging XDR and MDR Aeromonas veronii in Mugil seheli.

Aeromonas veronii is associated with substantial economic losses in the fish industry and with food-borne illness in humans. This study aimed to determine the prevalence, antibiogram profiles, sequence analysis, virulence and antimicrobial resistance genes, and pathogenicity of A. veronii recovered from Mugil seheli. A total of 80 fish were randomly gathered from various private farms in Suez Province, Egypt. Subsequently, samples were subjected to clinical, post-mortem, and bacteriological examinations. The retrieved isolates were tested for sequence analysis, antibiogram profile, pathogenicity, and PCR detection of virulence and resistance genes. The prevalence of A. veronii in the examined M. seheli was 22.5 % (18/80). The phylogenetic analyses revealed that the tested A. veronii strains shared high genetic similarity with other A. veronii strains from India, UK, and China. Using PCR it was revealed that the retrieved A. veronii isolates harbored the aerA, alt, ser, ompAII, act, ahp, and nuc virulence genes with prevalence of 100%, 82.9%, 61.7%, 55.3%, 44.7%, 36.17%, and 29.8%, respectively. Our findings revealed that 29.8% (14/47) of the retrieved A. veronii strains were XDR to nine antimicrobial classes and carried blaTEM, blaCTX-M, blaSHV,tetA, aadA1, and sul1 resistance genes. Likewise, 19.1% (9/47) of the obtained A. veronii strains were MDR to eight classes and possessed blaTEM, blaCTX-M, blaSHV,tetA, aadA1, and sul1 genes. The pathogenicity testing indicated that the mortality rates positively correlated with the prevalence of virulence-determinant genes. To our knowledge, this is the first report to reveal the occurrence of XDR and MDR A. veronii in M. seheli, an emergence that represents a risk to public health. Emerging XDR and MDR A. veronii in M. seheli frequently harbored aerA, alt, ser, ompAII, and act virulence genes, and blaTEM, sul1, tetA, blaCTX-M, blaSHV, and aadA1 resistance genes.

Phenotypic and genotypic antibiotic resistance patterns in Salmonella Typhimurium and its monophasic variant from pigs in southern Spain

The high incidence of human salmonellosis and multi-drug resistant (MDR) strains of Salmonella Typhimurium (ST) is of concern to global public and animal health. Our research, by means of the broth microdilution method, evaluated the Minimum Inhibitory Concentration (MIC) distribution of 12 antimicrobials against a collection of 73 ST and mST and S. typhimurium monophasic variant 4,[5],12:i:- (mST) isolates from slaughtered pigs reared in extensive systems in southern Spain, and also 12 resistance-associated genes or antimicrobial resistance (AMR) determinants using qPCR.Our data revealed that 98.6% of strains were MDR, with resistance to cephalothin/tetracycline/sulfamethoxazole-trimethoprim/ampicillin/chloramphenicol being the most common pattern (55.6%). Regarding AMR determinants, the most significantly (p < 0.05) genes detected by qPCR were sul1 and aadA2 (89% of strains positive), aadA1 and dfrA12 (87.7%), and blaTEM and tet(B) (86.3% and 84.9%, respectively).Up to date information on ST antimicrobial resistance patterns is essential for epidemiological surveillance programs to support animal and public health. The high number of MDR isolates and variability regarding resistance determinants revealed in this study highlights the role of animals reared in extensive systems as a source of resistant Salmonella strains.

Predominance of the East-Asian Beijing genotype in a Mycobacterium tuberculosis drug-resistant population in Central Malaysia

ObjectivesPrevious diversity studies on local Mycobacterium tuberculosis (MTB) isolates, with or without antibiotic resistance, showed predominance of Indo-Oceanic East African-Indian (EAI) strains. This study focused specifically on a drug-resistant MTB population from Central Malaysia and aimed to investigate the genotypes and resistance patterns involved. MethodsWhole-genome sequencing was performed on 56 local MTB isolates with known rifampicin resistance or multidrug resistance towards 13 anti-TB agents. Analysis of each genome sequence was performed using the widely recognized online MTB genotyping platforms, TBProfiler and Mykrobe, to determine lineage and genotypic drug resistance profiles. Results: Forty (71.4%) isolates were identified as East-Asian Beijing strains. Phenotypic to genotypic antibiotic resistance patterns differed in 33 isolates (58.9%), with one isolate showing extensive drug-resistance (XDR) previously not detected by conventional drug-susceptibility testing. ConclusionThis drug resistance population study demonstrated predominance of the East-Asian Beijing strains and a newly detected extensively drug-resistant MTB (XDR-TB) isolate in Malaysia. Information regarding the association between lineage and drug-resistant TB in Malaysia is scarce, and more studies are needed to determine the significance of such association, if any, in our local settings.

Susceptibility pattern in methicillin-resistant Staphylococcus aureus (MRSA) isolated from bovine mastitis

The study was conducted to determine the phenotypic and genotypic antimicrobial resistance pattern of methicillin resistant Staphylococcus aureus (MRSA) isolates from bovine mastitis. A total of 160 milk samples were collected aseptically from mastitis affected cows at organized dairy farms in and around Jammu and were subjected to microbial culture for the isolation and identification of methicillin resistant S. aureus using Baird Parker Agar. Out of the total 52 Staphylococcus aureus isolates, methicillin resistance (MRSA) was recorded in only 17 (32.69%) isolates out of which 7 (41.17%) isolates carried mecA gene. Susceptibility pattern of the MRSA isolates to other antibiotics revealed highest sensitivity towards enrofloxacin (100%) and lowest towards penicillin (5.88%). Multidrug resistance (MDR) was observed in 82.35% MRSA isolates. It is concluded that enrofloxacin is the most effective drug against mastitis in terms of sensitivity but undue use of the drug must be avoided to prevent the development of resistance against this drug in the near future. Hence, accurate diagnosis of bovine mastitis along with the correct selection of antibiotic is the key to prevent this devastating disease in dairy cows.&nbsp;

Study on antibiotic resistance and phylogenetic comparison of avian-pathogenic Escherichia coli (APEC) and uropathogenic Escherichia coli (UPEC) isolates.

Avian pathogenic Escherichia coli (APEC) and uropathogenic E. coli (UPEC) can cause vast infections in humans and poultry. The present study was conducted to compare the isolates of the APEC and UPEC pathotypes on the basis phenotypic and genotypic features of antibiotic resistance and phylogenetic differences. Total number of 70 identified E. coli strains, including 35 APEC and 35 UPEC isolates, were isolated from avian colibacillosis and human urinary tract infection (UTI), and were subjected to the antimicrobial susceptibility testing, polymerase chain reaction (PCR) detection of the resistance genes, phylogenetic grouping and DNA fingerprinting with enterobacterial repetitive intergenic consensus PCR (ERIC - PCR) to survey the variability of the isolates. The most resistance rates among all E. coli isolates were, respectively, obtained for Ampicillin (84.20%) and sulfamethoxazole-trimethoprim (65.70%). The APEC and UPEC isolates showed the most susceptibility to imipenem and gentamycin,respectively. Among 70 APEC and UPEC isolates 34.20%, 32.80%, 20.00%, and 12.80% belonged to the A, B2, D, and B1 phylogenetic groups, respectively. Analysis of the DNA fingerprinting phylogenetic tree showed 10 specific clusters of APEC and UPEC isolates. According to the results, the most effective antibiotics and the phenotypic and genotypic predominant resistance patterns of the APEC and UPEC isolates were different. Moreover, APECs and UPECs showed various dominant phylogenetic groups. With all descriptions, the APEC isolates still are potential candidates for carrying important resistance genes and can be one of the possible strains related to human infections.

Isolation and molecular characterization of multidrug-resistant Salmonella enterica serovars

BackgroundSalmonellosis is a foodborne zoonosis leaving gastrointestinal illness and drug-resistant genes to the consumers. To prevent Salmonella contamination associated health issues in the chicken meat sold in Riyadh city in Saudi Arabia. The evaluation of the Salmonella isolates from the meat sample needs to be screened for the composition of Salmonella serotypes and antimicrobial resistance pattern at the molecular level. Methods and resultsUsing specific growth media for Salmonella spp., swabs taken from the whole-body surfaces of 200 chilled broiler chickens from different vendors in the city of Riyadh, were screened for Salmonella contamination. Biochemical and molecular characterization of the isolates showed the presence of the serovars, Salmonella enterica, Salmonella Enteritidis, S. Typhimurium, S. Kentucky, and S. Tennessee. The isolated serovars exhibited multidrug resistance [MDR] resistance to antibiotics. Molecular characterization of the different serovars shows the presence of sixteen drug-resistant genes. The drug resistance mechanism at the molecular level varied with serotypes according to the nature of the antibiotics they encountered. A comparative study of the nature of the drug-resistant gene and the common antibiotics used in poultry farming in that province matches much, indicating adaptive variation in S. enterica serotypes to survive in the host's gut biome. The resistance genes from the chicken meat have every chance to get into the human system. The native microbes in consumers may acquire drug-resistant genes from S. entericus serovars. Such conditions may lead to treatment complications in the hosts. ConclusionsThe results indicated that Salmonella infections constituted a potential risk to consumers through chicken flocks and noted that the genotypic resistance pattern to antibiotics draws attention in terms of both human and animal health. Also, promote other options for poultry farming, avoiding antibiotics supplementation.

Detection of aerobic bacterial pathogens associated with early embryonic death in pregnant New Zealand female Rabbits in Egypt.

Background and Aim:Rabbits are a highly sensitive species and susceptible to various bacterial pathogens that may be causative agents for early embryonic death. This study aimed to explore the administration of different bacterial agents in does suffering from early embryonic death. Furthermore, identification of genes associated with virulence was performed to identify the phenotypic and genotypic antimicrobial resistance patterns that may increase the virulence of pathogens and lead to early embryonic death.Materials and Methods:We isolated and identified bacterial agents in 106 samples from live and dead female rabbits that had undergone early embryonic death, including liver and intestine tissue, aborted fetuses, discharges, and vaginal swabs. Conventional polymerase chain reaction (PCR) was conducted to confirm the identity of the isolated bacterial strains and their virulence. Moreover, antibiotic resistance was studied phenotypically and genotypically.Results:We isolated Escherichia coli, Salmonella, Staphylococcus aureus, Pasteurella multocida, and Listeria monocytogenes. PCR confirmed typical identification except in P. multocida, which was confirmed as Gallibacterium spp. in some cases. The final percentage of detection was 34%, 30.2%, 16.9%, 13.2%, and 11.3%, respectively. Virulence properties were investigated using different designated genes. All Salmonella strains harbored invA, stn, avrA, and ompf genes, while the sopE gene was identified in 31.25%. E. coli strains harboring the iss gene lacked the shiga toxin (stx1) gene. L. monocytogenes and S. aureus strains harbored the hemolysin gene (66.7% and 33.4%, respectively). Multidrug resistance was detected phenotypically and genotypically in most strains. Each bacterial pathogen had a different antibiotic resistance profile.Conclusion:Multiple bacterial species may contribute to early embryonic death in does. Furthermore, the combined infection could be the main cause of early embryonic death. Thus, monitoring programs should bear this in mind and focus on the early detection of these bacterial agents in female rabbits to avoid embryonic death.

Concordance of genotypic resistance interpretation algorithms in HIV-1 infected patients: An exploratory analysis in Greece.

Genotypic resistance-related mutations in HIV-1 disease are often difficult to interpret. Different algorithms have been developed to provide meaningful application into clinical context. We aimed to compare, for the first time in Greece, the results of genotypic resistance derived from three interpretation algorithms. The sequences of 120 HIV 1-infected patients were tested for genotypic resistance to 19 antiretroviral (ARV) drugs (n = 2280 sequences). The interpretation results of Rega, ANRS and ViroSeq algorithms were compared. Complete concordance was found for 2/19 ARV drugs, namely lamivudine and emptricitabine. Concordance was high for nucleoside reverse transcriptase inhibitors (NRTIs) and low for protease inhibitors (PIs). In inter-algorithm pairs, agreement was high between Rega and ViroSeq (kappa = 0.701), especially by ARV class, namely NRTIs (k = 0.869) and NNRTIs (k = 0.562). The only exception was noted for rilpivirine, where agreement was higher between ANRS and Rega (k = 0.410) compared to other inter-algorithm pairs (k = 0.018-0.055). By contrast, for PIs all comparisons yielded concordance equivalent to chance (k = 0.000). Our exploratory analysis provided evidence of significant inter-algorithm discordances, especially for PIs and NNRTIs highlighting the importance of matching the results of different algorithms to achieve optimized risk stratification. Ongoing research could assist clinical physicians in interpreting complex genotypic resistance patterns.

Phenotypic and Genotypic Antibiotic Resistance Patterns in Helicobacter pylori Strains From Ethnically Diverse Population in México.

Helicobacter pylori strains carry a range of mutations in genes that confer antimicrobial resistance and restrict the available options to treat the infection. Latin America is a region that conserve a large number of indigenous communities relatively isolated that practice a traditional medicine without consumption of drugs. We hypothesized that rates of antibiotic resistance are lower in these communities. Recent progress in whole-genome sequencing has allowed the study of drug susceptibility by searching for the known mutations associated with antibiotic resistance. The aim of this work was to study trends of antibiotic resistance over a 20-year period in Mexican H. pylori strains and to compare susceptibility between strains from Mexican mestizos and from indigenous population; we also aimed to learn the prevalence of mutational patterns in genes gyrA, gyrB, rdxA, frxA, rpsU, omp11, dppA, and 23S rRNA and its association with phenotypic tests. Resistance to clarithromycin, metronidazole, amoxicillin and levofloxacin was determined in167 H. pylori isolates by E-test, and the occurrence of mutational patterns in specific genes was determined by whole genome sequencing (WGS). The trend of resistance over 20 years in mestizo isolates showed significant resistant increase for clarithromycin and levofloxacin to frequencies that banned its clinical use. Resistance in H. pylori isolates of native communities was lower for all antibiotics tested. Phenotypic resistance showed good to moderate correlation with genotypic tests. Genetic methods for characterizing antibiotic resistance require further validation in each population.