Mohammad Jubair

International Centre for Diarrhoeal Disease Research, Bangladesh | ICDDR,B · Infectious Diseases Unit

In response to antibiotic and/or environmental stress, some species of bacteria shift to a "persister" phenotype. Although toxigenic Vibrio cholerae, responsible for the disease cholera, can be found in nutrient-poor aquatic environments in endemic areas, the underlying mechanism(s) by which culturable cells persist in these environmental reservoir...

Toxigenic Vibrio cholerae, ubiquitous in aquatic environments, is responsible for cholera; humans can become infected after consuming food and/or water contaminated with the bacterium. The underlying basis of persistence of V. cholerae in the aquatic environment remains poorly understood despite decades of research. We recently described a "persist...

Bangladesh experienced a long wave of the SARS-CoV-2 Omicron variant for the last one year, and it is still circulating throughout the country even though in small numbers. There were over 500 sub-lineages of this variant circulating globally, but not one had been shown as deadly as the previous variants. The question is whether the Omicron is the...

Background and Aims Saliva samples are less invasive and more convenient for patients than naso‐ and/or oropharynx swabs (NOS). However, there is no US Food and Drug Administration‐approved severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) rapid antigen test kit, which can be useful in a prolonged pandemic to reduce transmission by allow...

Background The global pandemic caused by SARS‐CoV‐2 has underlined the significance of strict genomic surveillance to track virus evolution and the possible emergence of new variants, particularly in densely populated countries like Bangladesh. This study outlines a strategic framework of genomic surveillance to track the evolution of the virus in...

The first case of COVID-19 was detected in Bangladesh on 8 March 2020. Since then, the Government of Bangladesh (GoB) has implemented various measures to limit the transmission of COVID-19, including widespread testing facilities across the nation through a laboratory network for COVID-19 molecular testing. This study aimed to analyze the dynamics...

Children carrying Staphylococcus aureus in their nasopharynx are at a higher risk of contracting systemic infection. Due to lack of sufficient information regarding such carriage, this study was conducted to explore the prevalence, antibiotic susceptibility, and genomic profiles of S. aureus isolated from nasopharyngeal samples of 163 randomly sele...

Introduction Early life soil-transmitted helminth infection and diarrhea are associated with growth faltering, anemia, impaired child development, and mortality. Exposure to fecally contaminated soil inside the home may be a key contributor to enteric infections, and a large fraction of rural homes in low-income countries have soil floors. The obje...

Background and aims The 2023 dengue outbreak in Bangladesh marked an unprecedented increase in fatalities, particularly in Dhaka, and demonstrated extensive prevalence nationwide, including Rajshahi district. Dengue fever remains a significant public health challenge in Southeast Asia, with complex epidemiological patterns. Previous research has ma...

Background: Lytic phages have been considered as a solution to mitigate the emergence of multidrug-resistant bacteria. Nevertheless, finding phages capable of targeting a broad host-range remains a significant challenge. Materials and Methods: Our study introduces two lytic phages isolated from hospital effluent, which are active against extended-s...

Staphylococcus aureus (SA) is an opportunistic pathogen and human commensal that is frequently present in the upper respiratory tract, gastrointestinal tract, and on the skin. While SA can cause disease ranging from minor skin infections to life-threatening bacteremia, it can also be carried asymptomatically. Indigenous individuals in the Southwest...

Candida auris, initially identified in 2009, has rapidly become a critical concern due to its antifungal resistance and significant mortality rates in healthcare-associated outbreaks. To date, whole-genome sequencing (WGS) has identified five unique clades of C. auris, with some strains displaying resistance to all primary antifungal drug classes....

We report 18 coding-complete genome sequences of emerging SARS-CoV-2 Omicron sub-lineages JN.1, JN.1.4, and JN.1.11 from Bangladesh. Nasopharyngeal swab samples were obtained from individuals with COVID-19 symptoms between December 2023 and January 2024. Whole genome sequencing was performed following the ARTIC Network-based protocol using Oxford N...

Candida auris , initially identified in 2009, has rapidly become a critical concern due to its antifungal resistance and significant mortality rates in healthcare-associated outbreaks. To date, whole-genome sequencing (WGS) has identified five unique clades of C. auris , with some strains displaying resistance to all primary antifungal drug classes...

Background. Despite use of highly effective conjugate vaccines, invasive pneumococcal disease (IPD) remains a leading cause of morbidity and mortality and disproportionately affects Indigenous populations. Although included in the 13-valent pneumococcal conjugate vaccine (PCV13), which was introduced in 2010, serotype 3 continues to cause disease a...

Antimicrobial resistance (AMR) in bacteria poses a global health emergency due to limited treatment options. Here, we report a lytic bacteriophage belonging to Stephanstirmvirinae family against an AMR Escherichia coli (ST2089). Escherichia phage iGC_PHA_EC001 is of genus Phapecoctavirus and 148,445 bp in length, encoding 269 predicted protein-codi...

Antimicrobial resistance (AMR) in bacteria poses a global health emergency due to limited treatment options. Here, we report a lytic bacteriophage belonging to Stephanstirmvirinae family against an AMR Escherichia coli (ST2089). Escherichia phage iGC_PHA_EC001 is of genus Phapecoctavirus and 148,445 bp in length, encoding 269 predicted protein-codi...

The emergence of multidrug-resistant (MDR) bacteria is a grave global health issue, and the time for studying the problem has passed; finding solutions is now crucial. Lytic bacteriophage or phage has been proposed as a promising alternative to antibiotics for combatting MDR. Selling antibiotics without a prescription, improper dosing, incomplete c...

We announce the coding-complete genomes of four different strains of SARS-CoV-2 Omicron lineages, XBB.1.16, XBB.2.3, FL.4 (alias of XBB.1.9.1.4), and XBB.3. These strains were obtained between October 2022 and May 2023 from nasopharyngeal swabs of four Bangladeshi individuals, while one of them had a travel history. Genomic data were produced by im...

The emergence of multidrug-resistant bacteria has become a significant global health concern, and lytic bacteriophage or phage has been proposed as a promising alternative. Nevertheless, finding phages capable of targeting a broad range of hosts remains a significant challenge. Our study introduces two lytic phages—iPHaGe-KPN-11i and iPHaGe-KPN-12i...

Background: Despite use of highly effective conjugate vaccines, invasive pneumococcal disease (IPD) remains a leading cause of morbidity and mortality and disproportionately affects Indigenous populations. Although included in the 13−valent pneumococcal conjugate vaccine (PCV13), which was introduced in 2010, serotype 3 (ST3) continues to cause dis...

Background and Aims The coronavirus disease 2019 (COVID‐19) has brought serious threats to public health worldwide. Nasopharyngeal, nasal swabs, and saliva specimens are used to detect severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). However, limited data are available on the performance of less invasive nasal swab for testing COVID‐19...

We announce the complete genomes of nine Streptococcus pneumoniae strains belonging to serotype 3 clonal complex 180 (CC180). The genomes consist of a single circularized contig with an average length of 2.033 Mbp. Pangenome analysis identified 1,762 core genes and 412 accessory genes. These genomes are the basis for future population genomic studi...

Background Globally, real‐time reverse transcription–polymerase chain reaction (rRT‐PCR) is the reference detection technique for SARS‐CoV‐2, which is expensive, time consuming, and requires trained laboratory personnel. Thus, a cost‐effective, rapid antigen test is urgently needed. This study evaluated the performance of the rapid antigen tests (R...

Staphylococci producing exfoliative toxins are the causative agents of staphylococcal scalded skin syndrome (SSSS). Exfoliative toxin A (ETA) is encoded by eta, which is harbored on a temperate bacteriophage ΦETA. A recent increase in the incidence of SSSS in North America has been observed; yet it is largely unknown whether this is the result of h...

Here, we announce the complete genome sequence of an exfoliative toxin-producing strain of Staphylococcus aureus sequence type 582 (ST582), isolated from a case of staphylococcal scalded-skin syndrome. The genome consists of a single circularized unitig with a total length of 2,792,190 bp carrying 2,699 genes. The genome is the basis for future epi...

Florida peaches (Prunus persica L.) are typically picked and placed in a cold room on the day of harvest, then packed and shipped on the next day. This room cooling (RC) is very slow, requiring approximately 24 h or more for the fruit to reach optimal temperature. There is currently limited research on the effect of cooling practices on microbial q...

Here, we present the draft genome sequence of Verrucosispora sp. strain CWR15, a bacterial symbiont of a Gulf of Mexico sponge. The genome consists of 35 contigs encoding 5,840 genes. The genome is the basis for future study and presents an underexplored taxonomy and biosynthetic potential.

In press: Prevention of microbial cross-contamination during postharvest handling is an important step to minimize microbial food safety hazards of produce. Dump tanks and flume systems are widely used in many states (e.g., Florida) to transfer/wash tomatoes, and are one of the most critical points where cross-contamination may occur. This study p...

The Food Safety Modernization Act attempts to reduce produce-related foodborne illness by using preventive rather than reactive measures. The goal of this research was to determine the persistence of manure-borne generic Escherichia coli under laboratory and field conditions. The population density of naturally occurring E. coli was ~7.2 and 5.4 lo...

Peaches can be damaged by rough handling, especially when picked at their advanced (tree ripe) stages. Current room cooling procedure used by peach growers often result in delays up to >12 h, possibly compromising quality. Determine the efficacy of postharvest room cooling on microbial quality control during peach storage. Peaches, harvested from d...

Prevention of microbial cross-contamination during postharvest handling is an important step to minimize microbial food safety hazards. Dump or flume tanks, which are widely used in Florida packinghouses to transfer/wash tomatoes, are one critical point for spreading cross-contamination. The main objective of this study conducted during the 2013-20...

Vibrio cholerae is ubiquitous in aquatic environments, with environmental toxigenic V. cholerae O1 strains serving as a source for recurrent cholera epidemics and pandemic disease. However, a number of questions remain about long-term survival and evolution of V. cholerae strains within these aquatic environmental reservoirs. Through monitoring of...

Introduction: Prevention of microbial cross-contamination during postharvest handling is an important step to minimize the microbial food safety hazards. Dump tanks (i.e., flume systems) are widely used in states like Florida to transfer/wash tomatoes, and are one of the most critical points where cross-contamination can be prevented. Purpose: The...

Unlabelled: Phylodynamic analysis of genome-wide single-nucleotide polymorphism (SNP) data is a powerful tool to investigate underlying evolutionary processes of bacterial epidemics. The method was applied to investigate a collection of 65 clinical and environmental isolates of Vibrio cholerae from Haiti collected between 2010 and 2012. Characteri...

In October, 2010, epidemic cholera was reported for the first time in Haiti in over 100 years. Establishment of cholera endemicity in Haiti will be dependent in large part on the continued presence of toxigenic V. cholerae O1 in aquatic reservoirs. The rugose phenotype of V. cholerae, characterized by exopolysaccharide production that confers resis...

Noroviruses (NoVs) are one of the major etiological agents of acute gastroenteritis in all age groups. In this study, we identified an intergenotype NoV recombinant strain in the fecal specimens of two male infants with acute diarrhea in Bangladesh. Phylogenetic analysis showed that the identified strains were recombinant NoV strains with a GII.3 c...