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Aims: Investigate the genetic stability of the BCG vaccine produced in Iran from different batches compared to the reference strain., Methods and Results: We comparatively analyzed the whole genome sequences of the vaccine batches from different years. Eleven vials of different batches from 2010, 2018, and 2019 were included. Complete genome analyses revealed no difference between the old (2010) and new (2018 and 2019) vaccine batches. Additionally, minor genetic changes include five single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) were observed compared to the BCG Pasteur 1173P2 reference strain, which were shared among all batches. Besides, the batches were identical to the reference strain in terms of antibiotic resistance genes, prophage sequences, and clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) systems., Conclusions: High genetic stability of the BCG vaccine used in the national immunization program was confirmed, which indicates the optimal conditions in the vaccine production process., Significance and Impact of the Study: Genetic differences within and between vaccine strains have been declared as one of the main parameters related to the BCG vaccine variable protective efficacy. No study has been done to investigate the genetic variations of the vaccine batches at the single-base level., (© 2021 The Society for Applied Microbiology.)

Objectives: To analyse the context of genes conferring antibiotic resistance in two carbapenem-resistant Acinetobacter baumannii isolates recovered in Tehran, Iran., Methods: The antibiotic resistance phenotype for 28 antibiotics was determined using disc diffusion. The whole genome sequences of ABH008 and ABS200 were determined using the Illumina HiSeq X Ten platform. Resistance genes were identified using ResFinder and multilocus sequence types were determined using the Oxford and Institut Pasteur schemes., Results: Isolates ABH008 and ABS200, recovered in 2012 and 2013, respectively, in two different Tehran hospitals, belong to the common global clone 1 lineage, ST1 IP and ST231 OX . They are resistant to sulfamethoxazole, tetracycline, gentamicin, amikacin, third-generation cephalosporins and carbapenems. Despite being isolated in different hospitals, phylogenetic analysis indicated they are closely related. Consistent with this, both isolates carry catA1, sul1, aacC1 and aadA1 in a novel variant of the AbaR3-type resistance island, named AbaR31. Both isolates are resistant to amikacin and carbapenems owing to aphA6 and oxa23 , respectively. The oxa23 gene is located in the AbaR4 resistance island, and aphA6 in Tn aphA6 , and both mobile elements are in an ∼90 kbp plasmid encoding the putative RepAci6 replication initiation protein. Resistance to third-generation cephalosporins is due to the acquisition by homologous recombination of a 5 kb DNA segment that contains ISAba1- ampC from a ST623 strain., Conclusions: The resistance gene complements of ABH008 and ABS200 were found in AbaR31 and a plasmid that encodes RepAci6. The close genetic relationship of ABH008 and ABS200, despite each being recovered from different hospitals, indicates transmission between the two hospitals., (© The Author(s) 2021. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.)

Stenotrophomonas maltophilia isolates are responsible for various hospital-acquired infections and are particularly increasing in the immunocompromised patients. The aim of this study was to determine the clonal relatedness between S. maltophilia isolates originating from the clinic and environment. A total of 150 S. maltophilia isolates from patients and 1108 environmental samples obtained in three hospitals from Tehran. Following molecular identification targeting 23S rRNA gene, the clonal relatedness of the environmental and clinical isolates was determined using pulsed field gel electrophoresis (PFGE). Of the 150 clinical and 18 environmental isolates identified using phenotypic tests, the speciation of 120 and 15 was confirmed by targeting the 23S rRNA gene. The 24 common pulsotypes (PTs) and 32 single PTs were identified by PFGE. Only a small cluster was shared among the clinic and environment within a hospital; therefore, the intra-hospital dissemination of certain isolates of S. maltophilia among the clinic and environment was demonstrated., (© 2020 The Society for Applied Microbiology.)

This study was set to determine the genetic linkage and the clonal relationship between vancomycin-resistant Enterococcusfaecium (VREfm) isolates in three hospitals of Ahwaz city. In this study, 1050 samples were collected from various rectal swabs, hands of health care workers, environmental surfaces, medical equipment and 146 enterococci isolates from clinical sources of three hospitals from March to September 2015. Antimicrobial resistance patterns in VREfm were detected by disk diffusion method. Genetic linkages of VREfm strains were investigated by pulse field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) methods. Out of 366 enterococcal isolates, 163 Enterococcus faecium isolates were found to be resistant to vancomycin. PFGE and MLST analysis showed the presence of 79 pulsotypes and 11 sequence types (ST), respectively. In total, 90% of the isolates belonged to clonal complex 17 (CC17). Three new STs were reported for the first time in this study and ST80 was the predominant ST. We found a high prevalence of diverse VREfm with threatening antibiotic resistance patterns in all the studied sources with the dominance of CC17 VREfm strains in Ahwaz hospitals. Also, the results of typing method showed inter- and intra-hospital circulation of VREfm and similar pulsotypes and STs among different sources., (© FEMS 2019.)

Aims: Little is known about the resistance rate and susceptibility profile of Clostridium difficile isolates in Iran. Therefore, the aim of present study is to assess the rate of drug-resistant C. difficile., Methods and Results: During a 6-year period, four hospitals submitted 735 stool specimens from patients suspected for C. difficile infections to the anaerobic bacteriology laboratory. The 46 C. difficile isolates were subjected to disc diffusion and minimum inhibitory concentration (MIC) Test Strips. All isolates were susceptible to vancomycin (VAN) while the highly resistant phenotypes of metronidazole (MTZ) (67·4%), moxifloxacin (78·3%), ciprofloxacin (69·5%) and tetracycline (82·6%) were observed. Of more concern, 67·3% of C. difficile isolates displayed multidrug-resistant phenotypes. More than half of the isolates (n = 27, 58·6%) were coresistant to ciprofloxacin and moxifloxacin. The MIC90 of VAN was ≤2 mg l -1 , whereas this value for MTZ, ciprofloxacin, moxifloxacin and tetracycline was higher than the resistance breakpoints. According to the comparison of interpretive categories for two tests, the categorical agreement was less than 90% for VAN, ciprofloxacin and tetracycline., Conclusions: The disc diffusion method can be used to detect the isolates with reduced susceptibility to MTZ or moxifloxacin. The high rate of resistance to fluoroquinolones highlights the possibility of the emergence of hypervirulent strains in our settings., Significance and Impact of the Study: This study provides data regarding the high level of resistance against multiple antibiotics except VAN., (© 2018 The Society for Applied Microbiology.)

In recent years, the increasing resistance of enteropathogenic Escherichia coli (EPEC) to commonly used antibiotics has made it difficult to choose the best treatment option. Bacteriophage therapy could be a potent alternative to antibiotic therapy for antibiotic-resistant bacteria. The aim of the present study was to isolate and identify a specific bacteriophage against EPEC and characterize bacteriophage in vitro and in vivo. The specific bacteriophage was isolated, and the effect of phage therapy on 48 mice (Balb/c) was investigated. Animals were divided into six groups, including A: PBS (negative control); B: bacteria (positive control); C: bacteria + ciprofloxacin (after 24 h); D: bacteria + bacteriophage (after 24 h); E: bacteria + ciprofloxacin + bacteriophage (after 24 h) and F: bacteriophage + bacteria (after 24 h). Specific bacteriophage against EPEC was isolated from hospital sewage. The bacteriophage had an icosahedral head (120 nm) and a tail (138 nm). The single dose of the bacteriophage (2 × 109 pfu ml-1) was able to control the infection. Unfortunately, because of the misuse of antibiotics by EPEC infected patients, the antibiotic resistant bacteria will become prevalent in the future and the treatment of EPEC infection is going to become more difficult than ever., (© FEMS 2018.)

The Acinetobacter baumannii virulence protein Bap is encoded by a large gene and contains both variable sequence and repetitive modules. To date, four primer sets targeting different regions of bap have been designed, but no study has evaluated all these primers simultaneously for detection of bap. Here, we assessed the effect of primer sets Bap I-IV, on detection of bap both in silico and in vitro. Using the primer set Bap II, all 143 tested strains yielded an amplicon corresponding to the bap gene. This primer set showed the highest sensitivity (100, 95% CI: 97·9-100%) compared to the other primer sets. This study demonstrates that primer set Bap II performs with optimal efficiency for detection of the bap gene among different strains., Significance and Impact of the Study: This study investigated the effect of nucleotide variation on PCR detection of the bap gene in various Acinetobacter baumannii strains. Since bap is the target gene for many detection assays, this variation can affect the detection efficiency. Here we present a primer set Bap II with optimal detection efficiency amongst 143 different strains, as shown by in silico and in vitro evidence., (© 2017 The Society for Applied Microbiology.)

Comprehensive data on drug-resistant patterns of Acinetobacter baumannii isolates in developing countries is limited. We conducted a multihospital study to assess the rate and trend of drug-resistant phenotypes in Ac. baumannii using standardized definitions and to determine the remaining therapeutic options against resistant phenotypes. The 401 nonduplicate isolates were collected from six hospitals which are geographically distributed across Tehran, Iran over a 3-year period. Following PCR of bla OXA -51-like gene, susceptibility testing was performed against nine antimicrobial agent categories. Three hundred and ninety (97%) isolates were resistant to least two carbapenems; carbapenem-resistant Ac. baumannii. The majority of isolates (366, 91·3%) were extensively drug resistant (XDR) and the rest of the isolates were classified as multidrug resistant (26, 6·8%) and susceptible (9, 2·2%). The rate of XDR-AB slightly decreased from 93·8% in 2011 to 89·8% in 2013. A considerable decrease in resistance to doxycycline, minocycline and tigecycline was demonstrated. The XDR-AB isolates showed susceptibility to gentamicin (10·4%), tobramycin (23%), ampicilin-sulbactam (30·1%), minocycline (32·8%), tigecycline (10·7%), doxycycline (21·6%), colistin (100%) and polymixin B (100%). We demonstrated the rising trend of resistance to all antibiotic categories except tetracyclines and folate pathway inhibitors. We found that the treatment options against XDR-AB are extremely limited and each treatment alternative including even old, but safe, antibiotics might be considered., Significance and Impact of the Study: The high frequency of drug-resistant phenotypes including carbapenem-resistant Acinetobacter baumannii, multidrug-resistant, and extensively resistant has been demonstrated in Ac. baumannii isolates tested here. As the antibiotic resistance pattern of isolates varies in different geographical regions, this study can provide comprehensive information about the antibiotic resistance profile of Ac. baumannii isolates in Tehran. In addition, the resistance profiles could be effectively considered by clinicians to manage antibiotic therapy. This work also emphasizes on the prudent use of antibiotics and the monitoring of antibiotic susceptibility trend and rate., (© 2016 The Society for Applied Microbiology.)

Aims: The aim of this multi-hospital study was to assess the in vitro activity of doripenem and its comparators, imipenem and meropenem, using the new CLSI breakpoints against a large population of a frequently isolated nosocomial pathogen, Acinetobacter baumannii., Methods and Results: During a 2-year period, four referral or tertiary hospitals submitted 400 isolates of Ac. baumannii for susceptibility testing using imipenem, meropenem and doripenem via disc diffusion and E-test methods. A subset of 390 isolates was resistant to all three tested carbapenems. Doripenem and meropenem (MIC50 , 32 μg ml(-1) ) had comparable activity, albeit doripenem's activity was greater than imipenem (MIC50 , >32 μg ml(-1) ). A significantly higher proportion of the isolates were inhibited by doripenem than by imipenem at MIC values of 12, 16, 24 and 32 μg ml(-1) (P < 0·05). The cumulative percentage of imipenem MICs was lower compared to its comparators. The comparison of resistance rate to imipenem and meropenem based on old and new breakpoints showed <1% difference. The overall agreement between the two susceptibility testing methods was ≥95%., Conclusion: Doripenem has a slightly greater in vitro activity than imipenem in terms of zone breakpoints and MIC values, but its activity is comparable to meropenem., Significance and Impact of the Study: Doripenem should be considered as a therapeutic option for monotherapy or combination therapy, particularly when the therapeutic options are limited., (© 2016 The Society for Applied Microbiology.)