Sherif Hamada

• PHD
• Al-Azhar University

The surge in mobile colistin-resistant genes (mcr) has become an increasing public health concern, especially in carbapenem-resistant Enterobacterales (CRE). Prospective surveillance was conducted to explore the genomic characteristics of clinical CRE isolates harbouring mcr in 2015–2020. In this study, we aimed to examine the genomic characteristi...

Background Escherichia coli is the most common cause of urinary tract infections and has fluoroquinolone (FQ)-resistant strains, which are a worldwide concern. Objectives To characterize FQ-resistant determinants among 103 carbapenem-resistant E. coli (CREc) urinary isolates using WGS. Methods Antimicrobial susceptibility, biofilm formation, and...

Understanding the survival strategies of pandemic cholera pathogens in aquatic environments is important for preventing their dissemination. Here, we report a phenomenon wherein long-term cultivation of Vibrio cholerae under nutrient-limited condition (M9 minimal medium supplemented with 0.2% glucose) causes mutations in flagella-related genes, thu...

Epidemiological surveys have shown that carbapenem resistance is mainly transmitted across species by carbapenemase genes located on conjugative plasmids. As chromosomal integration of carbapenemase genes has rarely been identified, only a few studies have investigated their advantages to the carbapenem-resistant bacterial community. Here, we confi...

Introduction. Carbapenemase-producing Enterobacteriaceae (CPE) have emerged as a global threat to public health and clinical practice. Hypothesis/Gap Statement. In Thailand, reports describing CPEs carrying bla NDM and bla OXA-48 -like genes have been increasing recently; however, data on detailed plasmid analysis and temporal shift of sequence typ...

Despite frequent identification of plasmids carrying carbapenemase genes, the transfer of plasmids carrying carbapenemase genes is not well recognized in clinical settings because of technical limitations. To investigate the detailed mechanisms of the spread of carbapenem-resistant Enterobacteriaceae (CRE), we performed multifaceted genomic surveil...

Carbapenem-resistant Enterobacterales (CRE) carrying bla NDM have spread worldwide since they were first reported in 2009. Many studies using whole-genome sequencing have identified the genetic structures, plasmid scaffolds of bla NDM , and mechanisms of spread via horizontal transfer.

Background Klebsiella pneumoniae ST258 and ST11 carrying blaKPC are among the most widespread carbapenem-resistant K. pneumoniae strains worldwide. Our carbapenem-resistant Enterobacteriaceae surveillance in Thailand revealed a nationwide dissemination of K. pneumoniae ST16 isolates carrying blaNDM-1 and blaOXA-232. Objectives To analyse the genom...

Heteroresistance is the phenomenon wherein subpopulations of presumed isogenic bacteria show varied antibiotic susceptibilities, and the current gold standard for heteroresistance determination is population analysis profiling (PAP). However, when we conducted PAP to confirm carbapenem-heteroresistance in Enterobacteriaceae, we found some isolates...

Carbapenem-resistant Enterobacterales (CRE) are a serious public health threat because of their rapid dissemination. To determine the epidemiological and genetic characteristics of CRE infections in Thailand, we performed whole-genome sequencing of 577 carbapenem-resistant Klebsiella pneumoniae isolates and 170 carbapenem-resistant Escherichia coli...

[This corrects the article DOI: 10.1093/ofid/ofaa492.].

Dissemination of the mobile colistin resistance gene mcr in Enterobacterales among humans, animals, and the environment is a public health issue. We characterized mcr genes in the Klebsiella pneumoniae complex (KpnC) isolated from slaughtered pigs in Thailand. The 280 KpnCs consisted of K. pneumoniae (85%), Klebsiella quasipneumoniae (8.21%), and K...

Carbapenem resistance is primarily conferred by carbapenemases, enzymes that hydrolyse carbapenems. While KPC, NDM and OXA-48 are the most commonly identified carbapenemases,¹ IMP carbapenemases have been frequently reported in Japan and Australia.²,³ In Japan, IMP-1 producers have disseminated predominantly in eastern areas, including Tokyo,⁴,⁵ an...

Introduction. The emergence and spread of non-typhoidal Salmonella enterica (NTS) serovars resistant to fluoroquinolones and third- and higher-generation cephalosporins is a matter of great concern. Antimicrobial-resistant NTS is increasingly being discovered in humans, animals, food animals, food products, and agricultural environments. Pigs are c...

The spread of vancomycin-resistant enterococci (VRE) is a major threat in nosocomial settings. A large-scale multiclonal VRE outbreak has rarely been reported in Japan due to low VRE prevalence. We evaluated the transmission of vancomycin resistance in a multiclonal VRE outbreak, conducted biological and genomic analyses of VRE isolates, and assess...

We demonstrated the multimerization of plasmids harboring carbapenemase genes, and multimeric plasmids of various discrete sizes existed in a host bacterial cell of Escherichia coli

Fifteen Klebsiella pneumoniae isolates harbouring bla NDM genes were identified from blood and sputum specimens of patients at a tertiary-care facility (Yangon General Hospital, Yangon, Myanmar) in 2018. Two of the isolates belonged to sequence type (ST) 11, an international high-risk clone. Whole-genome sequencing and phylogenetic analyses reveale...

Background: Carbapenemase-producing Enterobacterales (CPE) are spreading in hospitals, environment and retail foods in Yangon, Myanmar. Objectives: To investigate whether CPE colonize healthy individuals living in Yangon and whether clinical-related strains are spreading in the community. Methods: CPE was isolated from faecal samples obtained...

Carbapenem-resistant Acinetobacter pittii (CRAP) is a causative agent of nosocomial infections. This study aimed to characterize clinical isolates of CRAP from a tertiary hospital in Northeast Thailand. Six isolates were confirmed as extensively drug-resistant Acinetobacter pittii (XDRAP). The blaNDM-1 gene was detected in three isolates, whereas b...

The resistance of Enterobacteriaceae to colistin mediated by plasmid-borne mobile mcr genes is an emerging public health concern. This study aimed to explore the distribution and characteristics of Escherichia coli isolates harboring mcr genes from slaughtered pigs in Thailand from 2014 to 2015. A total of 779 E. coli isolates were assessed, of whi...

The resistance of Gram-negative bacteria to colistin, mediated by plasmid-borne mcr genes, is an emerging public health concern. The complete genome sequence (4.55 Mb) of a clinical isolate of Aeromonas veronii biovar veronii obtained from a patient with septicemia was determined using short-read and long-read platforms. This isolate (C198) was fou...

Background: Acinetobacter baumannii is recognized as a majority opportunistic nosocomial pathogen and caus-ing hospital-acquired infection worldwide. The increasing prevalence of extensively drug-resistant Acinetobacter baumannii (XDRAB) has become a rising concern in healthcare facilities and has impeded public health due to limitation of therapeu...

Global dissemination of carbapenem-resistant Enterobacteriaceae (CRE) threatens human health by limiting the efficacy of antibiotics even against common bacterial infections. Carbapenem resistance, mainly due to carbapenemase, is generally encoded on plasmids and is spread across bacterial species by conjugation. Most CRE epidemiological studies ha...

We performed whole-genome sequencing of Vibrio cholerae O1 isolates from Laos, Thailand, and Vietnam, where cholera outbreaks occurred, to determine their genetic lineages. Core genome phylogenetic analysis revealed that the isolates located in same lineage without regional clusters, which suggests that closely related strains circulated in Southea...

Shewanella sp., the progenitors of blaOXA‐48‐like genes are increasingly reported with the possession of different blaOXA‐48‐like variants. This study aims to characterize blaOXA‐731, a new variant of blaOXA‐48‐like gene identified in Shewanella sp. isolated from the aquatic environment in Myanmar. Phylogenetic analysis of the blaOXA‐731 sequence w...

Background. The global dissemination of carbapenem-resistant Enterobacteriaceae (CRE) threatens human health by limiting the range of usable antibiotics even against common bacterial infections. The spread of CRE is primarily due to the transmission of carbapenemase genes located on plasmids. However, few studies have comprehensively identified reg...

Many microbial species have been recognized as enteropathogens for humans. Here, we predicted the causative agents of acute diarrhea using data from multiplex quantitative PCR (qPCR) assays targeting 19 enteropathogens. For this, a case-control study was conducted at eight hospitals in Thailand. Stool samples and clinical data were collected from 3...

Introduction. Among the causative agents of bloodstream infections (BSIs), methicillin-resistant Staphylococcus aureus (MRSA) or vancomycin-resistant Enterococcus (VRE) are the key causative pathogens. Their rapid detection directly from Gram-positive cocci-positive blood culture specimens will promote timely treatment and help to implement effecti...

Background: Limited treatment options complicate management of infections with New Delhi metallo-β-lactamase (NDM)-producing organisms. We assessed the efficacy of combination therapy with meropenem (MEM) and cefmetazole (CMZ) against NDM-producing Enterobacteriaceae. Materials and methods: Twelve E. coli clinical isolates harbouring blaNDM-1 al...

The rapidly increasing prevalence of carbapenem-resistant Enterobacteriaceae (CRE) over the past decade has increased concern in healthcare facilities and the impact on public health. The prevalence of blaKPC (KPC) in Thailand remains very low; only blaKPC-13 has been described previously. This study is the first to describe the characteristics of...

Purpose. Carbapenemase-producing Enterobacteriaceae (CPE) have become a global concern and a serious threat to human health due to their resistance to multiple antibiotics. In this study, we identified and characterized CPE for the first time in Malawi, southeastern Africa.Methodology. We investigated the possible presence of carbapenemases among a...

The spread of carbapenemase-producing Enterobacteriaceae (CPE) poses a serious threat to clinical practice and public health. These bacteria are present both in clinical settings and non-clinical environments. The presence of CPE in food stuffs has been reported, but sporadically so. Here, we screened for CPE in meat, seafood, and vegetable samples...

Objectives: To analyse plasmids carrying blaIMP-6 in isolates of Klebsiella pneumoniae obtained from multicentre carbapenem-resistant Enterobacteriaceae surveillance. Methods: We characterised plasmids harbouring blaIMP-6 by the whole-genome sequencing of four K. pneumoniae isolates carrying blaIMP-6, and compared them with the pKPI-6 plasmid wi...

Background: Active surveillance has the potential to prevent nosocomial transmission of carbapenem-resistant Acinetobacter baumannii (CRAB). We assessed whether rapid diagnosis using clinical specimen-direct loop-mediated isothermal amplification (LAMP), a rapid molecular diagnostic assay, and subsequent intervention, could reduce CRAB nosocomial...

Colistin is used as an alternative therapeutic for carbapenemase-producing Enterobacteriaceae (CPE) infections which are spreading at a very high rate due to the transfer of carbapenemase genes through mobile genetic elements. Due to the emergence of mcr-1, the plasmid-mediated colistin resistance gene, mcr-1-positive Enterobacteriaceae (MCRPEn) po...

Acute diarrheal diseases are causes of global public health concern, especially in developing countries. A variety of diarrhea-associated microbial species, including bacteria, viruses, and protozoa, have been recognized. Simplified methods for detecting a wide range of diarrheagenic enteric microbes can clarify the etiology and aid in the diagnosi...

A multiplex PCR was described to simultaneously detect mcr-1 and frequently occurring carbapenem-resistant genes including blaKPC, blaNDM, blaIMP, and blaOXA-48-like in a single reaction. The PCR product sizes of these 4 carbapenem-resistant genes were 232 bp, 438 bp, 621 bp, and 798 bp for blaIMP, blaOXA-48-like, blaNDM, and blaKPC, respectively,...

Vibrio cholerae inhabits aquatic environments worldwide and has over 200 recognized serogroups classified by O-polysaccharide specificity. Here, we report that V. cholerae selects either of two genetic traits during their evolution. Sequencing of the specific gene locus MS6_A0927 revealed that 339 of 341 strains of V. cholerae and closely related V...

Purpose: The aim of this study was to develop a multiplex PCR (mPCR) for simultaneous detection (single reaction) of six clinically relevant streptococcal species: Streptococcus pneumoniae, Streptococcus suis, Streptococcus gallolyticus subsp. gallolyticus, S. gallolyticus subsp. pasteurianus, Streptococcus intermedius and Streptococcus anginosus/...

Cholera, caused by Vibrio cholerae, remains a global threat to public health. In Myanmar, the availability of published information on the occurrence of the disease is scarce. We report here that cholera incidence in Mandalay generally exhibited a single annual peak, with an annual average of 312 patients with severe dehydration over the past 5 yea...

A multiplex polymerase chain reaction (mPCR) was developed for simultaneous detection (single reaction) of genes specific to five frequent clinically relevant β-hemolytic streptococcal species: Streptococcus pyogenes (Spy1258), Streptococcus agalactiae (cfb and cpn60), Streptococcus dysgalactiae subsp. equisimilis (16S-23S intergenic spacer) , S. e...

Streptococcus suis, an important zoonotic pathogen, is known to have an open pan-genome and to develop a competent state. In S. suis, limited genetic lineages are suggested to be associated with zoonosis. However, little is known about the evolution of diversified lineages and their respective phenotypic or ecological characteristics. In this study...

Streptococcus suis is an important zoonotic pathogen in swine and humans that causes sepsis and meningitis. Our previous study in Thailand showed that the prevalence of S. suis infection in humans, especially in northern areas of Thailand, and the transmission of the pathogen occurred mainly through the consumption of traditional raw pork products....

To the Editor: Streptococcus suis is a zoonotic bacterium that causes invasive infections in humans and pigs (1). Of the 29 described serotypes, serotype 2 is the most prevalent in humans, almost exclusively affecting adults (1). Other serotypes occurring sporadically in humans have been reported (1). Here we report a rare case of S. suis serotype...

Multilocus sequence typing (MLST) is considered a reliable method for providing insight into the Streptococcus suis population structure, clonal relationships and the potential of particular clones to cause disease. Indeed, MLST has revealed the presence of several clonal complexes (CCs) within the Streptococcus suis population. However, the method...

Background Streptococcus suis is a zoonotic pathogen that causes invasive infections in humans and pigs. It has been reported that S. suis infection in humans is mostly caused by serotype 2. However, human cases caused by other serotypes have rarely been reported. This is the first report of a human case of infection with S. suis serotype 31 in Tha...

Group A Streptococcus (GAS) are globally distributed bacterial pathogens. We examined the emm genotypes, which are important indicators of virulence, of 349 clinical GAS isolates collected using two surveillance systems, i.e. Invasive Bacterial Infection Surveillance (IBIS) from 2010 to 2011 (234 isolates) and routine surveillance of clinically iso...

To the Editor: Prokaryotes typically have a single circular chromosome. However, some bacteria have >1 chromosome. Vibrio bacteria, for example, have 2 circular chromosomes: 1 (Ch1) and 2 (Ch2) (1–3). Most recognizable genes responsible for essential cell functions and pathogenicity are located on Ch1. Ch2 is also thought to encode some genes essen...

Streptococcus sanguinis, a member of the commensal mitis group of streptococci, is a primary colonizer of the tooth surface, and has been implicated in infectious complications including bacteremia and infective endocarditis. During disease progression, S. sanguinis may utilize various cell surface molecules to evade the host immune system to survi...

Background The cholera outbreaks in Thailand during 2007–2010 were exclusively caused by the Vibrio cholerae O1 El Tor variant carrying the cholera toxin gene of the classical biotype. We previously isolated a V. cholerae O1 El Tor strain from a patient with diarrhea and designated it MS6. Multilocus sequence-typing analysis revealed that MS6 is mo...

Introduction: Streptococcus suis, an emerging zoonotic pathogen, causes invasive infections in persons who are in close contact with infected pigs or contaminated pork-derived products. Although serotype 2 is the most prevalent type in S. suis infections in humans, to the best of our knowledge no human case caused by an unencapsulated strain has be...

We developed a practical and easy two-step multiplex PCR assay to aid in serotyping of Streptococcus suis. The assay accurately typed almost all of the serotype reference strains and field isolates of various serotypes and also identified the genotypes of capsular polysaccharide synthesis gene clusters of some serologically nontypeable strains.

A multiplex polymerase chain reaction (PCR) was developed to detect all true serotypes of Streptococcus suis. This multiplex PCR was composed of 4 reaction sets. The first set identified 9 serotypes (serotypes 1/2, 1, 2, 3, 7, 9, 11, 14 and 16), the second set identified 8 serotypes (serotypes 4, 5, 8, 12, 18, 19, 24 and 25), the third set identifi...

Background: Streptococcus suis is an emerging zoonotic pathogen, and causes sepsis and meningitis in humans. Although sequence type (ST) 1 and ST104 strains are capable of causing sepsis, ST1 strains commonly cause meningitis. In this study, we investigated the role of suilysin, a member of cholesterol-dependent cytolysins, in differential pathoge...

Field experiments were conducted in 2009–2010 and 2010–2011 seasons to evaluate the effect of four post-emergence clodinafop-propargyl formulations (Topic 15% WP, Akopic 24% EC, Current 24% EC and Herstop 15% WP) and hand weeding for controlling annual grassy weeds in wheat fields. Wheat seeds were sown in 25 and 30 November in both seasons, respec...

Streptococcus suis strains are classified into 35 serotypes on the basis of the antigenicity of their capsular polysaccharides (CPs). CP synthesis genes are known to be clustered on the chromosome (cps gene cluster). The entire cps gene clusters of S. suis have so far been sequenced in 15 serotypes and found to be located between orfZ and aroA. In...

A multiplex polymerase chain reaction (PCR) was developed to detect 15 serotypes of Streptococcus suis. This multiplex PCR was separated into 2 reaction sets. The first set identified 9 serotypes (serotypes 1/2, 1, 2, 3, 4, 7, 9, 14 and 16), and the second set identified 6 serotypes (serotypes 5, 8, 10, 19, 23 and 25). This assay correctly detected...

Group A Streptococcus pyogenes (GAS) is an important human pathogen that frequently causes pharyngitis. GAS organisms can adhere to and invade pharyngeal epithelial cells, which are overlaid by salivary components. However, the role of salivary components in GAS adhesion to pharyngeal cells has not been reported precisely. We collected human saliva...

Autophagy mediates the degradation of cytoplasmic contents in the lysosome and plays a significant role in immunity. Here we identified the small GTPases Rab9A and Rab23 as novel autophagy regulators during Group A streptococcus (GAS) infection. Rab9A was recruited to GAS-containing autophagosome-like vacuoles (GcAVs) after autophagosomal maturatio...

Streptococcus suis infection in humans has received increasing worldwide recognition. A prospective study of S. suis infection in humans was conducted in Phayao Province in northern Thailand to determine the incidence and the risk behaviors of the disease in this region in 2010. Thirty-one cases were confirmed. The case fatality rate was 16.1%, and...

Vibrio cholerae O1 El Tor dominated the seventh cholera pandemic which occurred in the 1960s. For two decades, variants of V. cholerae O1 El Tor that produce classical cholera toxin have emerged and spread globally, replacing the prototypic El Tor biotype. This study aims to characterize V. cholerae O1 isolates from outbreaks in Thailand with speci...

Minimum spanning tree of 343 Thai isolates and two reference strains of V. cholerae O1 typed by MLVA. Each circle in the trees represents a different MLVA type. The size of the circle reflects the number of isolates, and the colors indicate the proportion of isolates obtained during the year. MLVA types 22 and 46 (red circles) are reference strains...

PCR primers used in this study. (DOC)

Characterization of the V. cholerae O1 isolates used in this study. (XLS)

Pulsed-field gel electrophoresis of Thai outbreak isolates (pulsotypes A1 and B1) and reference Indian strains (pulsotypes H and H1). (EPS)

Relatedness of V. cholerae O1 El Tor variant isolates classified by several methods. (DOC)

The human pathogen Streptococcus pyogenes produces diverse pili depending on the serotype. We investigated the assembly mechanism of FCT type 1 pili in a serotype M6 strain. The pili were found to be assembled from two precursor proteins, the backbone protein T6 and ancillary protein FctX, and anchored to the cell wall in a manner that requires bot...

Streptococcus mutans is one of the oral pathogens associated with infective endocarditis (IE). With respect to bacterial binding ability to the extracellular matrix, the Cnm protein, a cell surface collagen-binding adhesin of S. mutans, is known as one of the possible virulence factors with regard to IE. In this study, we aimed to determine the dis...

Streptococcus pyogenes (group A streptococcus (GAS)) is a pathogen that invades non-phagocytic host cells, and causes a variety of acute infections such as pharyngitis. Our group previously reported that intracellular GAS is effectively degraded by the host-cell autophagic machinery, and that a cholesterol-dependent cytolysin, streptolysin O (SLO),...

Streptococcus pyogenes (group A streptococcus, GAS), one of the most common pathogens of humans, attaches and invades into human pharyngeal or skin epithelial cells. We have previously reported that induction of apoptosis is associated with GAS invasion, which induces mitochondrial dysfunction and apoptotic cell death. We demonstrate here that GAS-...

Cholera outbreaks occurred in Thailand in 2007. Isolates from the northeastern regions were analyzed. Interestingly, the outbreak strain was identified as biotype El Tor; serotype Ogawa with cholera toxin B subunit gene (ctxB) of the classical type and CTX prophage repressor gene of the El Tor type. The clone was genetically closely related to puls...

Streptococcus mutans is the major pathogen of dental caries, and it occasionally causes infective endocarditis. While the pathogenicity of this species is distinct from other human pathogenic streptococci, the species-specific evolution of the genus Streptococcus and its genomic diversity are poorly understood. We have sequenced the complete genome...

S. mutans NN2025 specific ORFs. Different regions within the PCR region are shown in different colours and correspond to the regions shown in Figure 2. No coloring in the PCR region indicates the absence of the ORF in the regions in Figure 2.

Cluster analysis based on strain-specific regions showing the relationship between S. mutans strain NN2025, UA159 and 95 clinical isolates. Long-PCR results were converted to numerical values according to the length of the PCR products, then complete linkage clustering was performed on CLUSTER software and visualized with Java Tree view software (c...

Distribution of CRISPR-2 (Smut2b)-associated repeat sequences in genus Streptococcus. Repeat sequences in the CRISPR-2 homologous region (Smut2b; Sthe3 family) found in streptococcal genomes except S. mutans NN2025 (15/31 strains; see Methods). Similarities were examined by BLASTN against each genome as a target database. The number of repeats was...

Genome comparison of each S. mutans with three S. agalactiae strains based on the chromosomal organization of the strain NN2025 or UA159. Dot plots of S. mutans NN2025 vs. three S. agalactiae strains and of S. mutans UA159 vs. the same set of S. agalactiae strains are presented, as generated by PROmer of MUMmer software and were visualized with the...

Lengths of locally collinear blocks (LCBs) shared by the nine Streptococcal species. Block lengths are taken from the S. mutans NN2025 genome. Lengths of LCBs were determined using SPRING software.

Long-PCR analyses of genomic rearrangement region and insertion/deletion regions of S. mutans strains.

Characteristics of S. mutans reference strains and clinical isolates used in this study.

Sequence similarities of the existing CRISPR spacers in S. mutans NN2025. The spacer similarities were determined by BLASTN against viruses including bacteriophage or bacteria databases (see Methods). No description in "origin" or "BLAST E-value" indicates that no similarity was found in the database.

Distribution of CRISPR-2 (Smut2b; Sthe3 family)-associated repeat sequences in genus Streptococcus. Repeat sequences in the CRISPR-2 homologous region (Sthe3 family) were found in 19 of 32 streptococcal genomes (see Methods; for NN2025, see additional file 8). Similarities of the direct repeat sequence of the strain NN2025 (Sthe3 family) were exami...

Specific gene groups shared in oral streptococci. All the predicted ORFs from the 32 streptococcal strains were clustered into groups based on a threshold of maximum E-value = 10-5 in the reciprocal BLATP analysis to extract the ORF(s) of gene groups specific for oral streptococci (S. mutans, S. sanguinis, and S. gordonii). The predicted function i...