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Introduction: Diphtheria caused by toxigenic Corynebacterium diphtheriae is an acute respiratory infection characterised by pseudomembrane formation in the throat. Although diphtheria is often reported sporadically across India, molecular characterisation of C.diphtheriae strains could play a crucial role in epidemiological investigations. Aim: To perform molecular characterisation of Corynebacterium diphtheriae isolates of faucial diphtheria cases from Assam, North-East India utilising Multi-Locus Sequence Typing (MLST). Materials and Methods: In this cross-sectional study, three isolates were obtained from three different cluster of cases that occurred across two districts of Assam, India for a period from November 2019 to June 2020. The MLST of these three C.diphtheriae isolates were performed in Multidisciplinary Research Unit of Assam Medical College and Hospital by using the 7-gene MLST alleles of C.diphtheriae to determine the Sequence Types (ST). Results: The MLST of the three isolates of this study revealed two distinct STs, ST-588 and ST-576 with multi-clonal lineages with ST-466, reported in C.diphtheriae strains of North Kerala and ST-301 related strains of Bangladesh, respectively. Conclusion: In spite of frequent reports of diphtheria cases from Assam, molecular typing of the C.diphtheriae strains found in North-Eastern region of India has not yet been performed. This is one of the initial investigations from this region of India to use MLST for typing C.diphtheriae strains. Therefore, studies related to molecular characterisation of C.diphtheriae strains found throughout India could immensely help in determining the clonality and diversity existing among these strains.

The worldwide spread of extended spectrum β-lactamase (ESBL)- and AmpC β-lactamase (AmpC)-producing Escherichia coli poses serious threats to public health. Swine farms have been regarded as important reservoirs of ESBL/AmpC-EC. This study aimed to determine the prevalence, ESBL/AmpC types, and clonal distribution of ESBL/AmpC-EC from swine farms and analyze the difference according to the swine production stages. In addition, we evaluated the potential risks of swine ESBL/AmpC-EC clones to humans. Individual fecal samples (n = 292) were collected from weaning, growing, finishing, and pregnant pigs in nine swine farms of South Korea between July 2017 and March 2020. In total, 161 ESBL/AmpC-EC isolates were identified (55.1%), with the highest prevalence detected in the weaning stage (86.3%). The dominant ESBL and AmpC types were CTX-M-55 (69.6%) and CMY-2 (4.3%), respectively. CTX-M found in all production stages, while CMY was only found in growing and finishing stages. In the conjugation assay, the high transferability of CTX-M gene (55.8%) was identified, while the transfer of CMY gene was not identified. The major clonal complexes (CCs) were CC101-B1 (26.8%), CC10-A (8.7%), and CC648-F (2.9%). There was similarity in clonal distribution between different swine production stages within swine farms, estimated using the k -means analysis, which suggested a clonal transmission between the different swine stages. Among swine ESBL/AmpC-EC sequence types (STs), seven STs (ST101, ST10, ST648, ST457, ST410, ST617, and ST744) were common with the human ESBL/AmpC-EC, which registered in National Center for Biotechnology Information database. The clonal population structure analysis based on the virulence factor (VF) presented that swine ESBL/AmpC-EC clones, especially ST101-B1, harbored a highly virulent profile. In conclusion, ESBL/AmpC-EC was distributed throughout the swine production stages, with the highest prevalence in the weaning stage. The CTX-M was present in all stages, while CMY was mostly found in growing-finishing stages. The swine ESBL/AmpC-EC was identified to harbor shared clone types with human ESBL/AmpC-EC and a virulent profile posing potential risk to humans. Considering the possibility of genetic and clonal distribution of ESBL/AmpC-EC among swine production stages, this study suggests the need for strategies considering the production system to control the prevalence of ESBL/AmpC-EC in swine farms. [ABSTRACT FROM AUTHOR]

Introduction: Diphtheria caused by toxigenic Corynebacterium diphtheriae is an acute respiratory infection characterised by pseudomembrane formation in the throat. Although diphtheria is often reported sporadically across India, molecular characterisation of C.diphtheriae strains could play a crucial role in epidemiological investigations. Aim: To perform molecular characterisation of Corynebacterium diphtheriae isolates of faucial diphtheria cases from Assam, North-East India utilising Multi-Locus Sequence Typing (MLST). Materials and Methods: In this cross-sectional study, three isolates were obtained from three different cluster of cases that occurred across two districts of Assam, India for a period from November 2019 to June 2020. The MLST of these three C.diphtheriae isolates were performed in Multidisciplinary Research Unit of Assam Medical College and Hospital by using the 7-gene MLST alleles of C.diphtheriae to determine the Sequence Types (ST). Results: The MLST of the three isolates of this study revealed two distinct STs, ST-588 and ST-576 with multi-clonal lineages with ST-466, reported in C.diphtheriae strains of North Kerala and ST-301 related strains of Bangladesh, respectively. Conclusion: In spite of frequent reports of diphtheria cases from Assam, molecular typing of the C.diphtheriae strains found in North-Eastern region of India has not yet been performed. This is one of the initial investigations from this region of India to use MLST for typing C.diphtheriae strains. Therefore, studies related to molecular characterisation of C.diphtheriae strains found throughout India could immensely help in determining the clonality and diversity existing among these strains. [ABSTRACT FROM AUTHOR]

Background: The clindamycin-resistant erythromycin-susceptible (CRES) phenotype is rare in Streptococcus agalactiae (group B streptococci). We aimed to determine the molecular characteristics of CRES S. agalactiae using whole genome sequencing (WGS). Methods: Sixty-six S. agalactiae isolates obtained from blood (N=26), cerebrospinal fluid (N=10), urine (N=17), and vaginal discharge (N=13) between 2010 and 2017 in Korea were subjected to WGS. Based on the WGS data, we analyzed antimicrobial resistance (AMR) determinants, sequence types (STs), capsular polysaccharide (CPS) genotypes, and virulence gene profiles, and constructed a phylogenetic tree. We included the clindamycin-susceptible erythromycin-resistant (CSER) phenotype for comparison. Results: We identified seven CRES S. agalactiae isolates from urine (N=5) and vaginal discharge (N=2) collected between 2010 and 2011. All CRES isolates harbored AMR determinants of lnu(B), lsa(E), and aac(6')-aph(2"), revealed ST19 and CPS genotype III, and had a virulence gene profile of rib-lmb-cylE. Phylogenetic tree analysis revealed that all CRES isolates belonged to the same cluster, suggesting a clonal distribution. In contrast, seven CSER isolates showed a diverse distribution and clustered separately from the CRES isolates. Conclusions: CRES isolates collected between 2010 and 2011 showed a unique cluster with ST19 and CPS genotype III in Korea. This is the first report on WGS-based characteristics of S. agalactiae in Korea. [ABSTRACT FROM AUTHOR]

Our objective was to improve current knowledge of sporadic (Spo) nosocomial Acinetobactercalcoaceticus-Acinetobacter baumannii (Acb) complex populations, and thus better understand the epidemiology of Spo and endemoepidemic (EE) strains. Between 1999 and 2010, 133 isolates of Spo Acb complex were obtained from a single hospital. Species were identified by gyrB-PCR, and via gyrB- and rpoB-sequencing. Clonal analysis was undertaken using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. Susceptibility to antimicrobial agents was determined by microdilution and E-tests. Carbapenemase genes were detected by PCR. One hundred and one PFGE types were detected. A. baumannii was the most common (67/101 PFGE types), followed by Acinetobacter pittii (22/101), Acinetobacter lactucae (6/101), and Acinetobacter calcoaceticus (2/101). gyrB, rpoB1, and rpoB2 sequencing returned 49, 13, and 16 novel sequences, respectively. Sixty-three sequence types (STs) (38 new STs and 66 new alleles) were detected; the most common were ST2 (29/133 isolates) and ST132 (14/133). Twenty-six OXA-51 allelic variants were detected, nine of which were novel. The PFGE types were generally susceptible (88/101) to all the tested antimicrobials; 3/101 were carbapenem-resistant due to the presence of the genetic structure ISAba2-blaOXA-58-like-ISAba3, and 2/101 were multidrug-resistant. It can be concluded that the examined Spo Acb complex population was mainly composed of A. baumannii. Many different clones were detected (with ST2 clearly dominant), all largely susceptible to antimicrobials; multidrug resistance was rare. In contrast, a previously examined EE Acb population was composed of just four expanding, multidrug-resistant A. baumannii clones -ST2, ST3, ST15, and ST80-.

Our objective was to improve current knowledge of sporadic (Spo) nosocomial Acinetobacter calcoaceticus-Acinetobacter baumannii (Acb) complex populations, and thus better understand the epidemiology of Spo and endemoepidemic (EE) strains. Between 1999 and 2010, 133 isolates of Spo Acb complex were obtained from a single hospital. Species were identified by gyr B-PCR, and via gyr B- and rpo B-sequencing. Clonal analysis was undertaken using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. Susceptibility to antimicrobial agents was determined by microdilution and E-tests. Carbapenemase genes were detected by PCR. One hundred and one PFGE types were detected. A. baumannii was the most common (67/101 PFGE types), followed by Acinetobacter pittii (22/101), Acinetobacter lactucae (6/101), and Acinetobacter calcoaceticus (2/101). gyr B, rpo B1, and rpo B2 sequencing returned 49, 13, and 16 novel sequences, respectively. Sixty-three sequence types (STs) (38 new STs and 66 new alleles) were detected; the most common were ST2 (29/133 isolates) and ST132 (14/133). Twenty-six OXA-51 allelic variants were detected, nine of which were novel. The PFGE types were generally susceptible (88/101) to all the tested antimicrobials; 3/101 were carbapenem-resistant due to the presence of the genetic structure IS Aba2 - bla OXA-58-like-IS Aba3 , and 2/101 were multidrug-resistant. It can be concluded that the examined Spo Acb complex population was mainly composed of A. baumannii. Many different clones were detected (with ST2 clearly dominant), all largely susceptible to antimicrobials; multidrug resistance was rare. In contrast, a previously examined EE Acb population was composed of just four expanding, multidrug-resistant A. baumannii clones -ST2, ST3, ST15, and ST80-. [ABSTRACT FROM AUTHOR]

Methicillin-resistant Staphylococcus pseudintermedius (MRSP) has emerged as an important health threat in companion animals, with potential for transmission to humans. However, little is known about MRSP circulating in Korea. Accordingly, in this study, we determined the prevalence, antimicrobial resistance profile' and clonal distribution of MRSP in Korea. Forty of 57 (70.17%) swab samples collected from dogs at five veterinary hospitals were positive for S. pseudintermedius (SP), and 21 dogs (36.84%) were carrying MRSP strains. Overall, 26 of 50 isolates (52.0%) were MRSP. Antimicrobial susceptibility tests against 18 antimicrobial agents (13 classes) revealed that all MRSP were multi-drug resistant isolates showing resistance to a wide range of antimicrobial classes. Compared to susceptible isolates, MRSP isolates showed higher resistance rates to most antimicrobials, including oxacillin (100%), cefazolin (96.2%), cefoxitin (96.2%), cefotaxime (100%), and trimethoprim-sulfamethoxazole (100%). Multilocus sequence typing revealed 27 distinct sequence types without a predominant type, including 22 novel types and 3 novel clonal complexes, indicating independently evolving lineages in Korea. Future studies on clones that will evolve to be a major clonal lineage in Korea could give us an important insight regarding the key factors related to the widespread of selected clones in the world. [ABSTRACT FROM AUTHOR]

Reliance on clonal reproduction is associated with an increased risk of extinction. Grevillea infecunda is a rare, putatively sterile shrub restricted to 11 populations in a localized coastal region of south-eastern Australia. We assessed the genetic diversity, clonal diversity and spatial distribution of clones in all populations of G. infecunda to guide conservation management. Eight chloroplast haplotypes were identified from the trnL - trnF and trnQ - rps16 intergenic spacer regions. All individuals belonged to a single maternal lineage dominated by one haplotype (95/111 samples). Minor haplotypes differed from the common haplotype only by single mutational steps. However, microsatellite markers revealed 89 multilocus genotypes (MLGs) in 38 multilocus lineages (MLLs) of variable size. MLLs were not shared among populations and ramets from different MLLs rarely intermingled physically. New shoots arising after fire were confirmed to belong to previously-existing MLLs, indicating that this species exhibits adaptation to fire. Genetically similar MLGs were more likely to be found in close proximity than less similar MLGs, resulting in significant spatial autocorrelation to ca 350 m. Genetic diversity was moderate but genotypic diversity was low once likely clonality was taken into account. Clonality appears to have arisen several times within the holly-leafed grevilleas and examining G. infecunda is a step towards understanding why and how often clonality occurs, and the long-term evolutionary outcomes of this life history. [ABSTRACT FROM AUTHOR]

The increasing burden of invasive biofilm-related staphylococcal infections has led to a dire need for new agents to prevent biofilm formation. Bacteriophages may hypothetically alter a biofilm through several mechanisms, including induction of depolymerizing enzymes and lysis of persistent bacteria. We have assessed the influence of commercially available bacteriophage cocktails on Staphylococcus spp. clinical strains viability and biofilm formation. We analyzed 83 staphylococcal strains from patients consecutively admitted to a Romanian infection reference center from October 2014 through May 2015; the strains were characterized by phenotypic and genetic tools for their resistance and virulence features and for their phyliation. Experiments were performed in triplicate. Methicillin-susceptible strains were significantly more susceptible to all tested phages: 1.7-fold higher susceptibility for PYO, 1.4-fold for INTESTI, 2.9-fold for PHAGYO, 2.7-fold for PHAGESTI and 3.9-fold for STAPHYLOCOCCAL; t030 strains were significantly more susceptible to PYO and INTESTI compared with t127 strains. We identified a significant decrease in biofilm formation in the presence of both low and high PYO and INTESTI concentrations (P < 0.001). In conclusion, Staphylococcus strains from Romania displayed fairly good susceptibility to commercially available bacteriophages. We have also ascertained there is phage-driven in vitro inhibition of biofilm formation, the results potentially impacting prevention of prosthetic infections. [ABSTRACT FROM AUTHOR]

Campylobacter jejuni bacteria are highly diverse enteropathogens. Seventy-three C. jejuni isolates from blood collected in Finland were analyzed by multilocus sequence typing and serum resistance. Approximately half of the isolates belonged to the otherwise uncommon sequence type 677 clonal complex. Isolates of this clonal complex were more resistant than other isolates to human serum.

The alien species Erigeron annuus (L.) Pers. is in an intensive spreading phase in Lithuania. Random amplified polymorphic DNA (RAPDs) and inter-simple sequence repeats (ISSRs) assays were used to study the genetic structure of old and new invasive populations and to determine the most spread genotypes of this species in Lithuania. Pairwise genetic distances between populations established using RAPD and ISSR markers significantly correlated (r=0.91, P<0.05). Our study indicates that there are two genetically different types of E. annuus populations. The first type is represented by a widely spread main clone and related monomorphic populations. The second type is represented by polymorphic populations, some of them present at sites where E. annuus has not been previously observed. Main clone predominates in nine populations and is from the region where this species was first described in natural ecosystems of Lithuania. UPGMA cluster analysis revealed genetic relationships between the main clone and accessions from old cemeteries where E. annuus has been grown as an ornamental plant. We found high genetic differentiation among populations ( G=0.58 for RAPDs, G=0.64 for ISSRs). Taken together, our results will contribute to the monitoring of E. annuus spread in Lithuania. [ABSTRACT FROM AUTHOR]

Willows of the Salix alba- Salix fragilis complex, native to western Eurasia, represent typical invaders of floodplain ecosystems worldwide. Introduced to South America by European settlers probably at the end of the nineteenth century, their distribution has increased significantly along the rivers in Northern Patagonia. This case study carried out mainly in the area around Lake Nahuel Huapi aims to analyze clonal structures and their spatial distribution using molecular markers as well as to relate the observed patterns to settlement history and life history traits of this species complex. Leaf material from 171 trees was collected along selected river floodplains in Northern Patagonia and genotypes were determined at six microsatellite loci. Including 62 reference samples of the S. alba- S. fragilis complex from German rivers, Probability of Identity ( P) was calculated and a Principal Coordinate Analysis (PCoA) conducted. From the altogether thirteen different genotypes detected, one dominant genotype (female) formed monoclonal stands along most of the studied river stretches. The maximum linear distance between the most remote ramets of this clone was 790 km. Evidence arose that the colonizing process so far is exclusively based on vegetative propagation in the focal study area and is obviously attributable to the pronounced brittleness of the hybrid parent S. fragilis. However, outside this area the occurrence of male trees and a diversity of genotypes indicate that evolutionary processes by recombination are involved within the willow complex. Therefore, an increase in genotypes can be assumed when male individuals and therefore sexual reproduction would appear in the area around Lake Nuhuel Huapi. This could be a crucial point for the long-term invasion success of the taxa when climatic and other environmental conditions will change in Southern Argentina. [ABSTRACT FROM AUTHOR]

This study evaluated the molecular epidemiology and biodiversity of Mycobacterium tuberculosis isolates in Zonguldak, Turkey, and investigated the presence and significance of the LAM7-TUR clone by spoligotyping and mycobacterial interspersed repetitive unit–variable number tandem repeat (MIRU-VNTR) analysis. In total, 128 isolates were tested by spoligotyping; 25 selected isolates representative of the LAM7-TUR clone and similar types were also tested by MIRU-VNTR analysis. In total, 47 distinct patterns were revealed by spoligotyping, represented by 13 clusters containing between two and 28 isolates (94 isolates in total), and 34 unique patterns (a clustering rate of 73%). Using MIRU-VNTR analysis, the clustering relationships revealed by spoligotyping were confirmed. The most common spoligotyping profile was SIT53, followed by SIT41 (LAM7-TUR) and SIT50. The SIT284 clone was another phylogeographically specific clonal complex whose presence in Turkey may be endemic. The LAM7-TUR genotype was highly prevalent in Zonguldak. [ABSTRACT FROM AUTHOR]

Reed stands in Germany and Europe were investigatedwith respect to their genetic diversity by means ofRandom Amplified Polymorphic DNA (RAPD) via thePolymerase Chain Reaction (PCR-fingerprinting).Different types of clonal distribution could bedistinguished: monoclonal reed stands and polyclonalreed stands, and among the latter, stands with low orhigh numbers of different clones as well as standswith mosaic-like coexisting or intermingling clones.Furthermore, clonal distribution and the expansion ofdifferent clones was observed within a newlydeveloping reed population. The findings appear tosupport a model of colonization postulating thatpopulations initiated by seeds are initiallygenetically diverse, but over time become dominated byone or a few clones adapted to the prevailing siteconditions. Thus, low genetic diversity seems to bethe result of a natural selection process. Clonaldiversity within a reed population and the type ofclonal distribution are discussed with regard to theirimportance for the reed stand's ability to adapt tochanging site conditions and eventually for itssurvival or die-back. [ABSTRACT FROM AUTHOR]

Campylobacter jejuni bacteria are highly diverse enteropathogens. Seventy-three C. jejuni isolates from blood collected in Finland were analyzed by multilocus sequence typing and serum resistance. Approximately half of the isolates belonged to the otherwise uncommon sequence type 677 clonal complex. Isolates of this clonal complex were more resistant than other isolates to human serum. [ABSTRACT FROM AUTHOR]

Background: The clindamycin-resistant erythromycin-susceptible (CRES) phenotype is rare in Streptococcus agalactiae (group B streptococci). We aimed to determine the molecular characteristics of CRES S. agalactiae using whole genome sequencing (WGS)., Methods: Sixty-six S. agalactiae isolates obtained from blood (N=26), cerebrospinal fluid (N=10), urine (N=17), and vaginal discharge (N=13) between 2010 and 2017 in Korea were subjected to WGS. Based on the WGS data, we analyzed antimicrobial resistance (AMR) determinants, sequence types (STs), capsular polysaccharide (CPS) genotypes, and virulence gene profiles, and constructed a phylogenetic tree. We included the clindamycin-susceptible erythromycin-resistant (CSER) phenotype for comparison., Results: We identified seven CRES S. agalactiae isolates from urine (N=5) and vaginal discharge (N=2) collected between 2010 and 2011. All CRES isolates harbored AMR determinants of lnu(B), lsa(E), and aac(6')-aph(2″), revealed ST19 and CPS genotype III, and had a virulence gene profile of rib-lmb-cylE. Phylogenetic tree analysis revealed that all CRES isolates belonged to the same cluster, suggesting a clonal distribution. In contrast, seven CSER isolates showed a diverse distribution and clustered separately from the CRES isolates., Conclusions: CRES isolates collected between 2010 and 2011 showed a unique cluster with ST19 and CPS genotype III in Korea. This is the first report on WGS-based characteristics of S. agalactiae in Korea.

We describe here a method to identify the position of retroviral insertion sites and simultaneously to quantify the absolute abundance of each clone, i.e., the number of cells having the provirus inserted at a given place in the host genome. The method is based on random shearing of the host cell DNA, followed by a linker-mediated PCR to amplify the genomic regions flanking the proviruses, and high-throughput sequencing of the amplicons. The quantification of the abundance of each infected clone allowed us to develop two new metrics: i. the oligoclonality index, which quantifies the nonuniformity of the distribution of clone abundance, and ii. an estimator of the total number of clones in the body of the host. These new tools are valuable for the study of retroviral infections and can also be adapted for the tracking of gene-edited cells.

Methicillin-resistant Staphylococcus aureus (MRSA) is a serious human pathogen that can cause a wide variety of infections. Comparative genetic analyses have led to the discovery that despite the existence of a vast number of genotypes, outbreak strains of MRSA appear to be limited to certain genotypes, some of which are further restricted to certain geographical locations. Whereas extensive literature is available in several countries, the complexity of the clonal distribution both of healthcare-associated (HA) and community-associated (CA) MRSA in India is only now beginning to be understood. Studies have revealed that MRSA in India is distributed among all of the major staphylococcal cassette chromosome mec (SCCmec) types. The majority of HA-MRSA isolates belong to SCCmec type III and sequence type (ST) 239. By contrast, CA-MRSA mostly belong to ST22 (SCCmec IV), ST772 (SCCmec V) and ST672 (SCCmec V) genotypes. Similar to the global scenario, CA-MRSA is becoming more invasive and transmissible and is increasingly becoming difficult to be differentiated from HA-MRSA. In addition, it is disturbing that some of the HA-MRSA isolates have been reported to be vancomycin-resistant. On the other hand, almost no information is available on the genotypes of livestock-associated MRSA or their potential impact on human infections in India. Concerted efforts are needed to further understand the genetic epidemiology of MRSA in India., (Copyright © 2016 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

This study addressed carbapenem-resistant Acinetobacter baumannii complex (ABC) isolates from patients that were injured during the military conflict in the Eastern Ukraine and treated at German Armed Forces Hospitals in 2014 and 2015. Clonal diversity of the strains and potential ways of transmission were analyzed. Patients with one or several isolation events of carbapenem-resistant ABC were included. Isolates were characterized by VITEK II-based identification and resistance testing, molecular screening for frequent carbapenemase genes, and DiversiLab rep-PCR-based typing. Available clinical information of the patients was assessed. From 21 young male Ukrainian patients with battle injuries, 32 carbapenem- and fluoroquinolone-resistant ABC strains were isolated. Four major clonal clusters were detected. From four patients (19%), ABC isolates from more than one clonal cluster were isolated. The composition of the clusters suggested transmission events prior to the admission to the German hospitals. The infection and colonization pressure in the conflict regions of the Eastern Ukraine with ABC of low clonal diversity is considerable. Respective infection risks have to be considered in case of battle-related injuries in these regions. The low number of local clones makes any molecular exclusion of transmission events difficult.